______  ____   ____  ____   ____  ______  __ __
    |      ||    \ |    ||    \ |    ||      ||  |  |
    |      ||  D  ) |  | |  _  | |  | |      ||  |  |
    |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
      |  |  |    \  |  | |  |  | |  |   |  |  |___, |
      |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
      |__|  |__|\_||____||__|__||____|  |__|  |____/

    Trinity-v2.15.2



Trinity version: Trinity-v2.15.2
-currently using the latest production release of Trinity.

Thursday, December 18, 2025: 09:06:12	CMD: /usr/local/bin/util/support_scripts/ensure_coord_sorted_sam.pl ../output/02.20-D-Apul-RNAseq-alignment-HiSat2/sorted-bams-merged.bam
-appears to be a coordinate sorted bam file. ok.
Thursday, December 18, 2025: 09:06:13	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /usr/local/bin/util/support_scripts/ExitTester.jar 0
Thursday, December 18, 2025: 09:06:13	CMD: java -Xmx4g -XX:ParallelGCThreads=2  -jar /usr/local/bin/util/support_scripts/ExitTester.jar 1
Thursday, December 18, 2025: 09:06:13	CMD: mkdir -p /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir


----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
----------------------------------------------------------------------------------

-found paired-end aligned read. Running in paired-end mode.
Thursday, December 18, 2025: 09:06:13	CMD: /usr/local/bin/trinity-plugins/bamsifter/bamsifter -c 200 -o /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/sorted-bams-merged.bam.norm_200.bam --keep_secondary /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/02.20-D-Apul-RNAseq-alignment-HiSat2/sorted-bams-merged.bam
Done with chr ntLink_7.
Done with chr ntLink_8.
Done with chr ntLink_0.
Done with chr ntLink_1.
Done with chr ntLink_2.
Done with chr ntLink_3.
Done with chr ntLink_4.
Done with chr ntLink_6.
Done with chr ptg000001l.
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Thursday, December 18, 2025: 11:59:40	CMD: touch /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/sorted-bams-merged.bam.norm_200.bam.ok
Thursday, December 18, 2025: 11:59:40	CMD: /usr/local/bin/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/sorted-bams-merged.bam.norm_200.bam -I 10000 --sort_buffer 100G --CPU 44  --SS_lib_type RF 
CMD: /usr/local/bin/util/support_scripts//SAM_strand_separator.pl /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/sorted-bams-merged.bam.norm_200.bam RF
CMD: /usr/local/bin/util/support_scripts//SAM_to_frag_coords.pl --CPU 44 --sort_buffer 100G --sam sorted-bams-merged.bam.norm_200.bam.+.sam --min_insert_size 1 --max_insert_size 10000 
CMD: /usr/local/bin/util/support_scripts//SAM_to_frag_coords.pl --CPU 44 --sort_buffer 100G --sam sorted-bams-merged.bam.norm_200.bam.-.sam --min_insert_size 1 --max_insert_size 10000 
-extracting read coordinates from sorted-bams-merged.bam.norm_200.bam.+.sam into sorted-bams-merged.bam.norm_200.bam.+.sam.read_coords

-extracting read coordinates from sorted-bams-merged.bam.norm_200.bam.-.sam into sorted-bams-merged.bam.norm_200.bam.-.sam.read_coords

CMD: touch sorted-bams-merged.bam.norm_200.bam.-.sam.read_coords.ok
CMD: /usr/bin/sort --parallel=44 -S100G -T . -k1,1 -k2,2 -k4,4n sorted-bams-merged.bam.norm_200.bam.-.sam.read_coords > sorted-bams-merged.bam.norm_200.bam.-.sam.read_coords.sort_by_readname
CMD: touch sorted-bams-merged.bam.norm_200.bam.+.sam.read_coords.ok
CMD: /usr/bin/sort --parallel=44 -S100G -T . -k1,1 -k2,2 -k4,4n sorted-bams-merged.bam.norm_200.bam.+.sam.read_coords > sorted-bams-merged.bam.norm_200.bam.+.sam.read_coords.sort_by_readname
CMD: cp /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/sorted-bams-merged.bam.norm_200.bam.-.sam.read_coords /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/sorted-bams-merged.bam.norm_200.bam.-.sam.read_coords.sort_by_readname
CMD: cp /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/sorted-bams-merged.bam.norm_200.bam.+.sam.read_coords /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/sorted-bams-merged.bam.norm_200.bam.+.sam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=44 -S100G -T . -k1,1 -k3,3n sorted-bams-merged.bam.norm_200.bam.+.sam.frag_coords > sorted-bams-merged.bam.norm_200.bam.+.sam.frag_coords.coord_sorted
CMD: /usr/bin/sort --parallel=44 -S100G -T . -k1,1 -k3,3n sorted-bams-merged.bam.norm_200.bam.-.sam.frag_coords > sorted-bams-merged.bam.norm_200.bam.-.sam.frag_coords.coord_sorted
CMD: /usr/local/bin/util/support_scripts//fragment_coverage_writer.pl sorted-bams-merged.bam.norm_200.bam.+.sam.frag_coords > sorted-bams-merged.bam.norm_200.bam.+.sam.frag_coverage.wig
CMD: /usr/local/bin/util/support_scripts//fragment_coverage_writer.pl sorted-bams-merged.bam.norm_200.bam.-.sam.frag_coords > sorted-bams-merged.bam.norm_200.bam.-.sam.frag_coverage.wig

[1000 lines read]  scaff:ntLink_0 lend:1109  rend:1243     
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[60000 lines read]  scaff:ntLink_3 lend:6781  rend:7226     
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[62000 lines read]  scaff:ntLink_3 lend:11571  rend:11860     
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[78000 lines read]  scaff:ntLink_3 lend:94684  rend:95265     
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[19551000 lines read]  scaff:ptg000010l lend:2251831  rend:2256709     
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[19552000 lines read]  scaff:ptg000010l lend:2259022  rend:2259159     
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[19553000 lines read]  scaff:ptg000010l lend:2261981  rend:2262116     
[17728000 lines read]  scaff:ptg000009l lend:1133634  rend:1133825     
[19554000 lines read]  scaff:ptg000010l lend:2267586  rend:2268108     
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[19563000 lines read]  scaff:ptg000010l lend:2308172  rend:2309629     
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[19567000 lines read]  scaff:ptg000010l lend:2324674  rend:2324897     
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[17754000 lines read]  scaff:ptg000009l lend:1264071  rend:1279480     
[19570000 lines read]  scaff:ptg000010l lend:2359388  rend:2359514     
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[19573000 lines read]  scaff:ptg000011l lend:84  rend:332     
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[19574000 lines read]  scaff:ptg000011l lend:470  rend:604     
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[17813000 lines read]  scaff:ptg000009l lend:1595759  rend:1596279     
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[21300000 lines read]  scaff:ptg000012l lend:2636527  rend:2636661     
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[21303000 lines read]  scaff:ptg000012l lend:2687967  rend:2688072     
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[19771000 lines read]  scaff:ptg000010l lend:1486156  rend:1486324     
[21305000 lines read]  scaff:ptg000012l lend:2694826  rend:2700603     
[19772000 lines read]  scaff:ptg000010l lend:1487046  rend:1487348     
[21306000 lines read]  scaff:ptg000012l lend:2701029  rend:2701393     
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[19773000 lines read]  scaff:ptg000010l lend:1488226  rend:1488382     
[19774000 lines read]  scaff:ptg000010l lend:1490286  rend:1491685     
[21308000 lines read]  scaff:ptg000012l lend:2729014  rend:2729715     
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[19776000 lines read]  scaff:ptg000010l lend:1503183  rend:1503350     
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[19778000 lines read]  scaff:ptg000010l lend:1517092  rend:1517409     
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[19782000 lines read]  scaff:ptg000010l lend:1559859  rend:1559993     
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[19791000 lines read]  scaff:ptg000010l lend:1594996  rend:1595124     
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[21319000 lines read]  scaff:ptg000012l lend:2810055  rend:2810300     
[21320000 lines read]  scaff:ptg000012l lend:2811113  rend:2811346     
[19794000 lines read]  scaff:ptg000010l lend:1636755  rend:1637444     
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[19803000 lines read]  scaff:ptg000010l lend:1703702  rend:1705872     
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[19805000 lines read]  scaff:ptg000010l lend:1710633  rend:1713467     
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[19806000 lines read]  scaff:ptg000010l lend:1714287  rend:1714561     
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[19808000 lines read]  scaff:ptg000010l lend:1719537  rend:1719897     
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[19810000 lines read]  scaff:ptg000010l lend:1723795  rend:1724153     
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[19841000 lines read]  scaff:ptg000010l lend:1904196  rend:1904522     
[19842000 lines read]  scaff:ptg000010l lend:1905446  rend:1905740     
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[21368000 lines read]  scaff:ptg000012l lend:3056081  rend:3060145     
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[19846000 lines read]  scaff:ptg000010l lend:1927811  rend:1928060     
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[19851000 lines read]  scaff:ptg000010l lend:1949877  rend:1950335     
[19852000 lines read]  scaff:ptg000010l lend:1952193  rend:1956226     
[21375000 lines read]  scaff:ptg000012l lend:3109480  rend:3113826     
[19853000 lines read]  scaff:ptg000010l lend:1979082  rend:1979362     
[19854000 lines read]  scaff:ptg000010l lend:1995715  rend:1995783     
[19855000 lines read]  scaff:ptg000010l lend:2015745  rend:2016301     
[21376000 lines read]  scaff:ptg000012l lend:3115634  rend:3116891     
[19856000 lines read]  scaff:ptg000010l lend:2017166  rend:2017478     
[19857000 lines read]  scaff:ptg000010l lend:2020459  rend:2020858     
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[19858000 lines read]  scaff:ptg000010l lend:2021362  rend:2021984     
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[19861000 lines read]  scaff:ptg000010l lend:2032125  rend:2036943     
[21380000 lines read]  scaff:ptg000012l lend:3151343  rend:3151492     
[19862000 lines read]  scaff:ptg000010l lend:2041705  rend:2042251     
[19863000 lines read]  scaff:ptg000010l lend:2043440  rend:2043574     
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[19872000 lines read]  scaff:ptg000010l lend:2142794  rend:2142977     
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[19873000 lines read]  scaff:ptg000010l lend:2161512  rend:2161682     
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[19876000 lines read]  scaff:ptg000010l lend:2168549  rend:2168815     
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[19878000 lines read]  scaff:ptg000010l lend:2175752  rend:2176095     
[21388000 lines read]  scaff:ptg000012l lend:3207498  rend:3207632     
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[19881000 lines read]  scaff:ptg000010l lend:2183436  rend:2183729     
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[19883000 lines read]  scaff:ptg000010l lend:2191222  rend:2191507     
[19884000 lines read]  scaff:ptg000010l lend:2193428  rend:2193507     
[19885000 lines read]  scaff:ptg000010l lend:2196698  rend:2196956     
[21390000 lines read]  scaff:ptg000012l lend:3218716  rend:3220935     
[19886000 lines read]  scaff:ptg000010l lend:2198930  rend:2199566     
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[19888000 lines read]  scaff:ptg000010l lend:2202169  rend:2202304     
[19889000 lines read]  scaff:ptg000010l lend:2204919  rend:2205053     
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[19891000 lines read]  scaff:ptg000010l lend:2231793  rend:2232244     
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[42946000 lines read]  scaff:ptg000026l lend:5708795  rend:5708929     
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[44988000 lines read]  scaff:ptg000027l lend:6656034  rend:6656179     
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[44991000 lines read]  scaff:ptg000027l lend:6716671  rend:6716805     
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[52814000 lines read]  scaff:ptg000105l lend:20328  rend:20462     
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[49507000 lines read]  scaff:ptg000035l lend:7795851  rend:7796583     
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[52849000 lines read]  scaff:ptg000108l lend:20  rend:99     
[49515000 lines read]  scaff:ptg000035l lend:7828004  rend:7828139     
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[49516000 lines read]  scaff:ptg000035l lend:7833235  rend:7833432     
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[52851000 lines read]  scaff:ptg000108l lend:4044  rend:8568     
[49518000 lines read]  scaff:ptg000035l lend:7839320  rend:7839456     
[49519000 lines read]  scaff:ptg000035l lend:7843063  rend:7843452     
[52852000 lines read]  scaff:ptg000108l lend:5978  rend:6112     
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[52855000 lines read]  scaff:ptg000108l lend:9248  rend:9382     
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[52861000 lines read]  scaff:ptg000108l lend:25641  rend:25775     
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[52865000 lines read]  scaff:ptg000108l lend:35256  rend:35380     
[52866000 lines read]  scaff:ptg000108l lend:38775  rend:38909     
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[52886000 lines read]  scaff:ptg000112l lend:4871  rend:5159     
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[52920000 lines read]  scaff:ptg000116l lend:683  rend:817     
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[49568000 lines read]  scaff:ptg000035l lend:8226823  rend:8227006     
[52936000 lines read]  scaff:ptg000116l lend:45938  rend:46135     
[49569000 lines read]  scaff:ptg000035l lend:8228916  rend:8229265     
[52937000 lines read]  scaff:ptg000117l lend:3944  rend:4256     
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[49572000 lines read]  scaff:ptg000035l lend:8233911  rend:8234305     
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[49576000 lines read]  scaff:ptg000035l lend:8240683  rend:8241181     
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[49577000 lines read]  scaff:ptg000035l lend:8241525  rend:8241640     
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[49580000 lines read]  scaff:ptg000035l lend:8244185  rend:8244885     
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[52953000 lines read]  scaff:ptg000120l lend:15238  rend:15912     
[49582000 lines read]  scaff:ptg000035l lend:8255652  rend:8255882     
[52954000 lines read]  scaff:ptg000120l lend:16433  rend:16875     
[52955000 lines read]  scaff:ptg000120l lend:18222  rend:18652     
[49583000 lines read]  scaff:ptg000035l lend:8257061  rend:8258338     
[52956000 lines read]  scaff:ptg000120l lend:22455  rend:22767     
[52957000 lines read]  scaff:ptg000121l lend:4211  rend:4465     
[49584000 lines read]  scaff:ptg000035l lend:8259275  rend:8260214     
[52958000 lines read]  scaff:ptg000121l lend:4803  rend:4896     
[52959000 lines read]  scaff:ptg000121l lend:5502  rend:5744     
[52960000 lines read]  scaff:ptg000121l lend:6371  rend:6505     
[49585000 lines read]  scaff:ptg000035l lend:8261872  rend:8262791     
[52961000 lines read]  scaff:ptg000121l lend:7229  rend:7363     
[52962000 lines read]  scaff:ptg000121l lend:8052  rend:8186     
[52963000 lines read]  scaff:ptg000121l lend:8640  rend:8774     
[52964000 lines read]  scaff:ptg000121l lend:9336  rend:9806     
[52965000 lines read]  scaff:ptg000121l lend:9895  rend:10001     
[52966000 lines read]  scaff:ptg000121l lend:10433  rend:10547     
[49586000 lines read]  scaff:ptg000035l lend:8268339  rend:8269479     
[52967000 lines read]  scaff:ptg000121l lend:14498  rend:14632     
[52968000 lines read]  scaff:ptg000121l lend:15041  rend:15229     
[52969000 lines read]  scaff:ptg000121l lend:27586  rend:27725     
[52970000 lines read]  scaff:ptg000121l lend:34751  rend:34886     
[49587000 lines read]  scaff:ptg000035l lend:8292397  rend:8292494     
[52971000 lines read]  scaff:ptg000121l lend:35484  rend:35591     
[52972000 lines read]  scaff:ptg000121l lend:36443  rend:36577     
[49588000 lines read]  scaff:ptg000035l lend:8319642  rend:8319775     
[52973000 lines read]  scaff:ptg000121l lend:37392  rend:37526     
[52974000 lines read]  scaff:ptg000121l lend:38274  rend:38689     
[49589000 lines read]  scaff:ptg000035l lend:8320572  rend:8320709     
[52975000 lines read]  scaff:ptg000121l lend:39027  rend:39161     
[52976000 lines read]  scaff:ptg000121l lend:39772  rend:40064     
[52977000 lines read]  scaff:ptg000121l lend:40403  rend:40831     
[52978000 lines read]  scaff:ptg000121l lend:41844  rend:41978     
[52979000 lines read]  scaff:ptg000121l lend:45235  rend:45369     
[49590000 lines read]  scaff:ptg000035l lend:8322730  rend:8327060     
[52980000 lines read]  scaff:ptg000122l lend:6547  rend:7050     
[52981000 lines read]  scaff:ptg000122l lend:8500  rend:8642     
[52982000 lines read]  scaff:ptg000122l lend:10070  rend:10597     
[52983000 lines read]  scaff:ptg000122l lend:11667  rend:12489     
[52984000 lines read]  scaff:ptg000122l lend:12910  rend:13301     
[49591000 lines read]  scaff:ptg000035l lend:8335718  rend:8341190     
[52985000 lines read]  scaff:ptg000122l lend:17516  rend:18196     
[52986000 lines read]  scaff:ptg000122l lend:26500  rend:26827     
[49592000 lines read]  scaff:ptg000035l lend:8336424  rend:8337064     
[49593000 lines read]  scaff:ptg000035l lend:8337566  rend:8337743     
[49594000 lines read]  scaff:ptg000035l lend:8338786  rend:8339008     
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[49596000 lines read]  scaff:ptg000035l lend:8340382  rend:8340516     
[49597000 lines read]  scaff:ptg000035l lend:8340864  rend:8340998     
[52987000 lines read]  scaff:ptg000122l lend:36247  rend:40305     
[49598000 lines read]  scaff:ptg000035l lend:8364428  rend:8364917     
[49599000 lines read]  scaff:ptg000035l lend:8370384  rend:8370528     
[49600000 lines read]  scaff:ptg000035l lend:8376515  rend:8377456     
[52988000 lines read]  scaff:ptg000123l lend:11806  rend:11946     
[49601000 lines read]  scaff:ptg000035l lend:8379432  rend:8380561     
[52989000 lines read]  scaff:ptg000123l lend:14851  rend:15307     
[49602000 lines read]  scaff:ptg000035l lend:8384055  rend:8384343     
[52990000 lines read]  scaff:ptg000123l lend:29742  rend:29892     
[49603000 lines read]  scaff:ptg000035l lend:8385359  rend:8386113     
[52991000 lines read]  scaff:ptg000124l lend:5588  rend:6106     
[49604000 lines read]  scaff:ptg000035l lend:8387580  rend:8387787     
[52992000 lines read]  scaff:ptg000124l lend:14707  rend:14842     
[49605000 lines read]  scaff:ptg000035l lend:8406831  rend:8407182     
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[49607000 lines read]  scaff:ptg000035l lend:8446491  rend:8446688     
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[49714000 lines read]  scaff:ptg000035l lend:9142488  rend:9142724     CMD: touch sorted-bams-merged.bam.norm_200.bam.+.sam.frag_coverage.wig.ok
CMD: /usr/local/bin/util/support_scripts//define_coverage_partitions.pl sorted-bams-merged.bam.norm_200.bam.+.sam.frag_coverage.wig 1 + > sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff

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[52761000 lines read]  scaff:ptg000054l lend:2309  rend:3095     
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[52766000 lines read]  scaff:ptg000055l lend:88  rend:574     
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[52768000 lines read]  scaff:ptg000055l lend:897  rend:1031     
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[52788000 lines read]  scaff:ptg000059l lend:76334  rend:76428     
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[52810000 lines read]  scaff:ptg000059l lend:323424  rend:323558     
[52811000 lines read]  scaff:ptg000059l lend:380621  rend:380800     
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[52845000 lines read]  scaff:ptg000063l lend:8629  rend:9308     
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[52856000 lines read]  scaff:ptg000065l lend:94  rend:476     
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[52862000 lines read]  scaff:ptg000066l lend:1415  rend:1549     
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[52888000 lines read]  scaff:ptg000069l lend:34031  rend:40437     
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[52896000 lines read]  scaff:ptg000070l lend:23115  rend:23323     
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[52901000 lines read]  scaff:ptg000070l lend:52271  rend:52405     
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[52912000 lines read]  scaff:ptg000070l lend:186060  rend:186181     
[52913000 lines read]  scaff:ptg000072c lend:1032  rend:1166     
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[52945000 lines read]  scaff:ptg000072c lend:55733  rend:71407     
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[52954000 lines read]  scaff:ptg000072c lend:72940  rend:118544     
[52955000 lines read]  scaff:ptg000072c lend:78893  rend:79027     
[52956000 lines read]  scaff:ptg000072c lend:79791  rend:79925     
[52957000 lines read]  scaff:ptg000072c lend:80665  rend:80799     
[52958000 lines read]  scaff:ptg000072c lend:81406  rend:81540     
[52959000 lines read]  scaff:ptg000072c lend:82501  rend:82635     
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[52961000 lines read]  scaff:ptg000072c lend:90485  rend:112459     
[52962000 lines read]  scaff:ptg000072c lend:91746  rend:91880     
[52963000 lines read]  scaff:ptg000072c lend:92773  rend:92965     
[52964000 lines read]  scaff:ptg000072c lend:93903  rend:94019     
[52965000 lines read]  scaff:ptg000072c lend:94590  rend:94724     
[52966000 lines read]  scaff:ptg000072c lend:95499  rend:95633     
[52967000 lines read]  scaff:ptg000072c lend:97128  rend:97231     
[52968000 lines read]  scaff:ptg000072c lend:102358  rend:102492     
[52969000 lines read]  scaff:ptg000072c lend:103536  rend:103670     
[52970000 lines read]  scaff:ptg000072c lend:104539  rend:104673     
[52971000 lines read]  scaff:ptg000072c lend:105811  rend:105954     
[52972000 lines read]  scaff:ptg000072c lend:107788  rend:108143     
[52973000 lines read]  scaff:ptg000072c lend:114367  rend:114501     
[52974000 lines read]  scaff:ptg000072c lend:116072  rend:116183     
[52975000 lines read]  scaff:ptg000072c lend:117590  rend:117724     
[52976000 lines read]  scaff:ptg000072c lend:125198  rend:125816     
[52977000 lines read]  scaff:ptg000072c lend:127409  rend:127543     
[52978000 lines read]  scaff:ptg000072c lend:128463  rend:128597     
[52979000 lines read]  scaff:ptg000072c lend:137678  rend:137812     
[52980000 lines read]  scaff:ptg000072c lend:139560  rend:139676     
[52981000 lines read]  scaff:ptg000072c lend:141138  rend:141265     
[52982000 lines read]  scaff:ptg000072c lend:150014  rend:150274     
[52983000 lines read]  scaff:ptg000072c lend:152037  rend:152171     
[52984000 lines read]  scaff:ptg000072c lend:153967  rend:154101     
[52985000 lines read]  scaff:ptg000072c lend:163888  rend:164027     
[52986000 lines read]  scaff:ptg000072c lend:166164  rend:166298     
[52987000 lines read]  scaff:ptg000072c lend:173132  rend:173266     
[52988000 lines read]  scaff:ptg000072c lend:175441  rend:175575     
[52989000 lines read]  scaff:ptg000072c lend:193349  rend:193483     
[52990000 lines read]  scaff:ptg000072c lend:196512  rend:196646     
[52991000 lines read]  scaff:ptg000072c lend:206617  rend:206751     
[52992000 lines read]  scaff:ptg000072c lend:208741  rend:208875     
[52993000 lines read]  scaff:ptg000072c lend:212459  rend:212770     
[52994000 lines read]  scaff:ptg000072c lend:222893  rend:223391     
[52995000 lines read]  scaff:ptg000072c lend:227122  rend:227256     
[52996000 lines read]  scaff:ptg000072c lend:239428  rend:239562     
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[53000000 lines read]  scaff:ptg000072c lend:263845  rend:264081     
[53001000 lines read]  scaff:ptg000072c lend:271025  rend:271159     
[53002000 lines read]  scaff:ptg000072c lend:272676  rend:272810     
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[53011000 lines read]  scaff:ptg000072c lend:350095  rend:350440     
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[53384000 lines read]  scaff:ptg000105l lend:73265  rend:73400     
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[53387000 lines read]  scaff:ptg000105l lend:79914  rend:80038     
[53388000 lines read]  scaff:ptg000106l lend:963  rend:1061     
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[53391000 lines read]  scaff:ptg000106l lend:8119  rend:10508     
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[53398000 lines read]  scaff:ptg000106l lend:34246  rend:34632     
[53399000 lines read]  scaff:ptg000107l lend:887  rend:1021     
[53400000 lines read]  scaff:ptg000107l lend:1266  rend:1400     
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[53411000 lines read]  scaff:ptg000107l lend:27903  rend:28670     
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[53446000 lines read]  scaff:ptg000109l lend:32728  rend:32862     
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[53448000 lines read]  scaff:ptg000112l lend:4299  rend:4433     
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[53452000 lines read]  scaff:ptg000112l lend:25022  rend:25509     
[53453000 lines read]  scaff:ptg000112l lend:31622  rend:31730     
[53454000 lines read]  scaff:ptg000113l lend:1719  rend:2136     
[53455000 lines read]  scaff:ptg000113l lend:10242  rend:10395     
[53456000 lines read]  scaff:ptg000113l lend:18818  rend:18955     
[53457000 lines read]  scaff:ptg000113l lend:21017  rend:21151     
[53458000 lines read]  scaff:ptg000113l lend:32774  rend:32916     
[53459000 lines read]  scaff:ptg000113l lend:41593  rend:42166     
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[53467000 lines read]  scaff:ptg000114l lend:2198  rend:7534     
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[53469000 lines read]  scaff:ptg000114l lend:22800  rend:22969     
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[53473000 lines read]  scaff:ptg000115l lend:5154  rend:5288     
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[53477000 lines read]  scaff:ptg000115l lend:34640  rend:34774     
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[53485000 lines read]  scaff:ptg000116l lend:40229  rend:40361     
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[53494000 lines read]  scaff:ptg000118l lend:27713  rend:28295     
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[53496000 lines read]  scaff:ptg000120l lend:8356  rend:8519     
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[53501000 lines read]  scaff:ptg000121l lend:11623  rend:11718     
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[53505000 lines read]  scaff:ptg000121l lend:35914  rend:36048     
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[53509000 lines read]  scaff:ptg000122l lend:23697  rend:23848     
[53510000 lines read]  scaff:ptg000122l lend:31731  rend:31865     
[53511000 lines read]  scaff:ptg000123l lend:14842  rend:15089     
[53512000 lines read]  scaff:ptg000123l lend:24989  rend:25292     
[53513000 lines read]  scaff:ptg000123l lend:25884  rend:26202     
[53514000 lines read]  scaff:ptg000123l lend:26814  rend:27068     
[53515000 lines read]  scaff:ptg000123l lend:27976  rend:28468     
[53516000 lines read]  scaff:ptg000123l lend:29912  rend:30078     
[53517000 lines read]  scaff:ptg000123l lend:31224  rend:31431     
[53518000 lines read]  scaff:ptg000124l lend:7909  rend:8703     
[53519000 lines read]  scaff:ptg000124l lend:11973  rend:12133     
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[53521000 lines read]  scaff:ptg000124l lend:31591  rend:36407     
[53522000 lines read]  scaff:ptg000124l lend:42930  rend:43740     
[53523000 lines read]  scaff:ptg000125l lend:5518  rend:6957     
[53524000 lines read]  scaff:ptg000125l lend:7045  rend:7515     
[53525000 lines read]  scaff:ptg000126l lend:12328  rend:12822     
[53526000 lines read]  scaff:ptg000127l lend:2609  rend:3109     
[53527000 lines read]  scaff:ptg000127l lend:3292  rend:3650     
[53528000 lines read]  scaff:ptg000127l lend:4216  rend:4350     
[53529000 lines read]  scaff:ptg000127l lend:22205  rend:22600     
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[53531000 lines read]  scaff:ptg000128l lend:739  rend:873     
[53532000 lines read]  scaff:ptg000128l lend:15657  rend:16045     
[53533000 lines read]  scaff:ptg000128l lend:16659  rend:16793     
[53534000 lines read]  scaff:ptg000128l lend:20303  rend:20436     
[53535000 lines read]  scaff:ptg000128l lend:33179  rend:35823     
[53536000 lines read]  scaff:ptg000128l lend:36167  rend:36718     
[53537000 lines read]  scaff:ptg000128l lend:37117  rend:37251     
[53538000 lines read]  scaff:ptg000129l lend:1273  rend:1407     
[53539000 lines read]  scaff:ptg000129l lend:4412  rend:4546     
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[53541000 lines read]  scaff:ptg000129l lend:10897  rend:11002     
[53542000 lines read]  scaff:ptg000129l lend:17535  rend:18251     
[53543000 lines read]  scaff:ptg000129l lend:23048  rend:23203     
[53544000 lines read]  scaff:ptg000129l lend:24930  rend:25697     
[53545000 lines read]  scaff:ptg000129l lend:28958  rend:29286     
[53546000 lines read]  scaff:ptg000129l lend:32853  rend:32998     
[53547000 lines read]  scaff:ptg000130l lend:7047  rend:7449     
[53548000 lines read]  scaff:ptg000130l lend:7708  rend:7842     
[53549000 lines read]  scaff:ptg000130l lend:12981  rend:13191     
[53550000 lines read]  scaff:ptg000130l lend:14283  rend:14624     
[53551000 lines read]  scaff:ptg000130l lend:20448  rend:20582     
[53552000 lines read]  scaff:ptg000130l lend:26974  rend:27108     
[53553000 lines read]  scaff:ptg000130l lend:29003  rend:29137     
[53554000 lines read]  scaff:ptg000130l lend:33065  rend:33144     
[53555000 lines read]  scaff:ptg000131l lend:7714  rend:7850     
[53556000 lines read]  scaff:ptg000132l lend:2183  rend:2355     
[53557000 lines read]  scaff:ptg000132l lend:7957  rend:14217     
[53558000 lines read]  scaff:ptg000132l lend:18683  rend:18890     
[53559000 lines read]  scaff:ptg000132l lend:20419  rend:21439     
[53560000 lines read]  scaff:ptg000133l lend:282  rend:704     
[53561000 lines read]  scaff:ptg000133l lend:1582  rend:2099     
[53562000 lines read]  scaff:ptg000133l lend:8474  rend:16006     
[53563000 lines read]  scaff:ptg000133l lend:15877  rend:16011     
[53564000 lines read]  scaff:ptg000133l lend:25586  rend:25720     
[53565000 lines read]  scaff:ptg000134l lend:46510  rend:65319     
[53566000 lines read]  scaff:ptg000134l lend:76901  rend:77040     
[53567000 lines read]  scaff:ptg000136l lend:4029  rend:4558     
[53568000 lines read]  scaff:ptg000136l lend:9809  rend:12761     
[53569000 lines read]  scaff:ptg000137l lend:2725  rend:2859     
[53570000 lines read]  scaff:ptg000137l lend:7677  rend:7811     
[53571000 lines read]  scaff:ptg000137l lend:15576  rend:15710     
[53572000 lines read]  scaff:ptg000137l lend:27559  rend:27834     
[53573000 lines read]  scaff:ptg000138l lend:73  rend:347     
[53574000 lines read]  scaff:ptg000138l lend:702  rend:878     
[53575000 lines read]  scaff:ptg000138l lend:1374  rend:1508     
[53576000 lines read]  scaff:ptg000138l lend:2050  rend:2184     
[53577000 lines read]  scaff:ptg000138l lend:2763  rend:2868     
[53578000 lines read]  scaff:ptg000138l lend:3601  rend:3923     
[53579000 lines read]  scaff:ptg000138l lend:4253  rend:4387     
[53580000 lines read]  scaff:ptg000138l lend:12118  rend:12252     
[53581000 lines read]  scaff:ptg000138l lend:12809  rend:12943     
[53582000 lines read]  scaff:ptg000138l lend:13673  rend:14159     
[53583000 lines read]  scaff:ptg000138l lend:14502  rend:14631     
[53584000 lines read]  scaff:ptg000138l lend:15432  rend:15566     
[53585000 lines read]  scaff:ptg000138l lend:16285  rend:16419     
[53586000 lines read]  scaff:ptg000138l lend:17014  rend:17148     
[53587000 lines read]  scaff:ptg000138l lend:26239  rend:26460     
[53588000 lines read]  scaff:ptg000138l lend:27213  rend:27347     
[53589000 lines read]  scaff:ptg000138l lend:28208  rend:28342     
[53590000 lines read]  scaff:ptg000138l lend:29104  rend:29384     
[53591000 lines read]  scaff:ptg000138l lend:30012  rend:30301     
[53592000 lines read]  scaff:ptg000138l lend:30849  rend:30983     
[53593000 lines read]  scaff:ptg000138l lend:33598  rend:33719     
[53594000 lines read]  scaff:ptg000140l lend:15152  rend:15538     
[53595000 lines read]  scaff:ptg000140l lend:15259  rend:15545     
[53596000 lines read]  scaff:ptg000140l lend:15754  rend:15801     
[53597000 lines read]  scaff:ptg000140l lend:16497  rend:16631     
[53598000 lines read]  scaff:ptg000140l lend:17320  rend:17868     
[53599000 lines read]  scaff:ptg000140l lend:19050  rend:19184     
[53600000 lines read]  scaff:ptg000141l lend:38692  rend:38826     
[53601000 lines read]  scaff:ptg000146l lend:11801  rend:12462     
[53602000 lines read]  scaff:ptg000146l lend:16994  rend:26535     
[53603000 lines read]  scaff:ptg000146l lend:38710  rend:39031     
[53604000 lines read]  scaff:ptg000158l lend:11137  rend:11266     
[53605000 lines read]  scaff:ptg000159l lend:14655  rend:15018     
[53606000 lines read]  scaff:ptg000159l lend:17563  rend:17720     
[53607000 lines read]  scaff:ptg000160l lend:6136  rend:6415     
[53608000 lines read]  scaff:ptg000160l lend:10541  rend:10747     
[53609000 lines read]  scaff:ptg000160l lend:14516  rend:15195     
[53610000 lines read]  scaff:ptg000160l lend:23311  rend:23445     
[53611000 lines read]  scaff:ptg000161l lend:5441  rend:5575     
[53612000 lines read]  scaff:ptg000162l lend:4858  rend:4992     
[53613000 lines read]  scaff:ptg000165l lend:5116  rend:5250     
[53614000 lines read]  scaff:ptg000165l lend:19693  rend:19797     
[53615000 lines read]  scaff:ptg000167l lend:1655  rend:1789     
[53616000 lines read]  scaff:ptg000169l lend:11412  rend:11661     
[53617000 lines read]  scaff:ptg000171l lend:33188  rend:33324     
[53618000 lines read]  scaff:ptg000172l lend:13236  rend:13265     
[53619000 lines read]  scaff:ptg000172l lend:33392  rend:33526     
[53620000 lines read]  scaff:ptg000172l lend:41582  rend:41716     
[53621000 lines read]  scaff:ptg000174l lend:8167  rend:8515     
[53622000 lines read]  scaff:ptg000175l lend:22566  rend:22889     
[53623000 lines read]  scaff:ptg000176l lend:19044  rend:19178     
[53624000 lines read]  scaff:ptg000176l lend:21548  rend:21678     
[53625000 lines read]  scaff:ptg000177l lend:9816  rend:9952     
[53626000 lines read]  scaff:ptg000177l lend:19495  rend:19745     
[53627000 lines read]  scaff:ptg000177l lend:40943  rend:41085     
[53628000 lines read]  scaff:ptg000179l lend:96  rend:211     
[53629000 lines read]  scaff:ptg000179l lend:3936  rend:4070     
[53630000 lines read]  scaff:ptg000179l lend:26879  rend:27000     
[53631000 lines read]  scaff:ptg000179l lend:38924  rend:39272     
[53632000 lines read]  scaff:ptg000180l lend:217  rend:320     
[53633000 lines read]  scaff:ptg000180l lend:1944  rend:2432     
[53634000 lines read]  scaff:ptg000180l lend:5160  rend:5753     
[53635000 lines read]  scaff:ptg000181l lend:18189  rend:18323     
[53636000 lines read]  scaff:ptg000181l lend:26819  rend:26952     
[53637000 lines read]  scaff:ptg000182l lend:23233  rend:23382     
[53638000 lines read]  scaff:ptg000183l lend:20265  rend:20311     
[53639000 lines read]  scaff:ptg000183l lend:25889  rend:26023     
[53640000 lines read]  scaff:ptg000184l lend:22091  rend:22220     
[53641000 lines read]  scaff:ptg000184l lend:27443  rend:27664     
[53642000 lines read]  scaff:ptg000184l lend:39899  rend:40033     
[53643000 lines read]  scaff:ptg000185l lend:22051  rend:22185     
[53644000 lines read]  scaff:ptg000186l lend:17495  rend:18090     CMD: touch sorted-bams-merged.bam.norm_200.bam.-.sam.frag_coverage.wig.ok
CMD: /usr/local/bin/util/support_scripts//define_coverage_partitions.pl sorted-bams-merged.bam.norm_200.bam.-.sam.frag_coverage.wig 1 - > sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff
CMD: touch sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff.ok
CMD: /usr/local/bin/util/support_scripts//extract_reads_per_partition.pl --partitions_gff sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff  --coord_sorted_SAM sorted-bams-merged.bam.norm_200.bam.+.sam --parts_per_directory 100 --min_reads_per_partition 10  --SS_lib_type RF 
// parsing paritions.

[100]  
[200]  
[300]  
[400]  
[500]  
[600]  
[700]  
[800]  
[900]  
[1000]  
[1100]  
[1200]  
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[1700]  
[1800]  
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[2000]  
[2100]  
[2200]  
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[2400]  
[2500]  
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[2800]  
[2900]  
[3000]  
[3100]  
[3200]  
[3300]  
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[3800]  
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[4000]  
[4100]  
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[4600]  
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[4800]  
[4900]  
[5000]  
[5100]  
[5200]  
[5300]  
[5400]  
[5500]  
[5600]  
[5700]  
[5800]  
[5900]  
[6000]  
[6100]  
[6200]  
[6300]  
[6400]  
[6500]  
[6600]  
[6700]  
[6800]  
[6900]  
[7000]  
[7100]  
[7200]  
[7300]  
[7400]  
[7500]  
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[7700]  
[7800]  
[7900]  
[8000]  
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[8200]  
[8300]  
[8400]  
[8500]  
[8600]  
[8700]  
[8800]  
[8900]  
[9000]  
[9100]  
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[9300]  
[9400]  
[9500]  
[9600]  
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[9800]  
[9900]  
[10000]  
[10100]  
[10200]  
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[10700]  
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[11800]  
[11900]  
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[12600]  
[12700]  
[12800]  
[12900]  
[13000]  
[13100]  
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[13300]  
[13400]  
[13500]  
[13600]  
[13700]  
[13800]  
[13900]  
[14000]  
[14100]  
[14200]  
[14300]  
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[14600]  
[14700]  
[14800]  
[14900]  
[15000]  
[15100]  
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[15800]  
[15900]  
[16000]  
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[16600]  
[16700]  
[16800]  
[16900]  
[17000]  
[17100]  
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[17400]  
[17500]  
[17600]  
[17700]  
[17800]  
[17900]  
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[19800]  
[19900]  
[20000]  
[20100]  
[20200]  
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[20500]  
[20600]  
[20700]  
[20800]  
[20900]  
[21000]  
[21100]  
[21200]  
[21300]  
[21400]  
[21500]  
[21600]  
[21700]  
[21800]  
[21900]  
[22000]  
[22100]  
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[22300]  
[22400]  
[22500]  
[22600]  
[22700]  
[22800]  
[22900]  
[23000]  
[23100]  
[23200]  
[23300]  
[23400]  
[23500]  
[23600]  
[23700]  
[23800]  
[23900]  
[24000]  
[24100]  
[24200]  
[24300]  
[24400]  
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[24600]  
[24700]  
[24800]  
[24900]  
[24959]  -writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_7/0/38_180836.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_7/0/180965_182916.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/18752_18886.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/31795_31932.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/36288_381106.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/382460_382767.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/382843_383150.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/383181_383651.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/384255_384580.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/386649_386785.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/388505_389475.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/389598_389904.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/404953_405161.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/406180_406484.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/406491_406639.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/406800_407006.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/408161_408233.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/410181_410450.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/410468_410860.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/411813_412982.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/415088_415658.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/415929_661703.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/661745_661879.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/662758_662933.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/663002_663099.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/664398_664545.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/664755_664939.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/665269_665624.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/665669_666023.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/666056_666282.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/666385_666615.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/667104_667175.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/667472_667665.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/667962_668088.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/668126_668546.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/668551_668759.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/669716_669850.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/669919_670047.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/670110_670344.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/670376_670592.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/670962_671176.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/671705_672297.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/679221_681484.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/681798_681996.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/682078_682235.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/683267_684075.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/685233_740977.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/741164_741292.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/742610_742921.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/743898_744051.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/745077_746003.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/746146_746379.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/746411_746545.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/747689_1166585.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1166665_1166749.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1167666_1167958.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1168568_1168876.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1169706_1169724.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1170350_1205104.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1208973_1209117.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1209144_1209348.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1209575_1210081.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1210190_1210931.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1213155_1213232.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1213248_1213627.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1214067_1214424.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1215669_1215815.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1216169_1216450.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1217796_1218033.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1221818_1226789.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1226916_1227302.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1227353_1227373.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1229576_1230776.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1230832_1231024.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1231930_1232072.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1237284_1237395.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1237999_1238259.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1238611_1239211.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1239385_1963039.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1965562_1966431.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1967414_1967548.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1967588_1967722.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1969051_1969341.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1969455_1969718.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1972954_1973113.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1978008_1978265.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1980416_1980678.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1982542_1983180.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1983881_1984042.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1984233_1985249.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/1985559_3908140.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/3908550_3909018.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/3909353_3909509.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/3913107_3913236.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/3913722_3913867.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/3914816_4699077.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/4699219_4699953.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/4699975_5193364.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_8/0/5193780_5193904.trinity.reads
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-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8674234_8678340.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8678437_8678571.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8678708_8679789.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8680042_8680267.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8680323_8680999.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8681004_8779733.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8779766_8781373.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8781385_8781572.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8781732_8781884.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8782233_8782371.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8782378_8782497.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8782589_8782743.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8783078_8783268.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8783355_8784110.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8784614_8785064.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8785616_8785750.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8785829_8788198.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8788535_8789302.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8789627_8792572.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8792585_8793187.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8793321_8793450.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8793453_8793782.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8793885_8794046.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8794742_8794855.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8795412_8795546.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8795961_8796482.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8797208_8797282.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8797348_8797805.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8798011_8798156.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8798764_8800473.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8800487_8800582.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8800894_8801167.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8801243_8801377.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8801463_8801671.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8802929_8803910.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8803964_8804098.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8804668_8805742.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8806356_8806490.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8806520_8806742.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8811354_8811647.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8811775_8812000.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8814881_8815015.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8815284_8815421.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8815459_8815622.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8817263_8817378.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8817457_8818733.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8819241_8819508.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8820417_8820543.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/2/8820672_8820949.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/8821194_8821708.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/8821872_8822178.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/8823750_8823994.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/8826203_8826325.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/8827932_9169777.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9170320_9171386.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9171684_9172134.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9172188_9172325.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9172660_9172829.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9174024_9174428.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9174902_9175488.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9176241_9189954.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9190191_9190893.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9191409_9191928.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9192324_9192487.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9194735_9195319.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9195380_9198300.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9198447_9209853.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9210956_9211345.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9211691_9218938.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9220901_9221050.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9221181_9221459.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9221905_9222088.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9223625_9223804.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9223847_9224336.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9225648_9225829.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9227333_9227983.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/9228664_10992362.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/10992437_10995289.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/10995303_10996028.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/10996064_10996255.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/10999742_10999877.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11000088_11000222.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11000372_11000506.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11000535_11000669.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11000673_11001261.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11004457_11004483.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11005889_11006074.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11007185_11007457.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11008851_11008934.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11011753_11011887.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11012666_11012780.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11013300_11019286.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11021327_11031763.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11032279_11033166.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11035691_11035866.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11039344_11039422.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11040689_11040934.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11041267_11041403.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/11043518_12171466.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/12171479_12171644.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/12171689_12172269.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/12172714_12173040.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/12173268_12173673.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/12174990_12175128.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/12175477_12197017.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/12198036_12198170.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/12201384_12378038.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/12381094_13105409.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/13106499_14144616.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/14146792_14147884.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/14149552_15394898.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15394900_15395263.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15395382_15395624.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15395790_15396157.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15397614_15399758.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15399863_15400116.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15400268_15400745.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15400939_15401027.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15401339_15401625.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15401868_15402355.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15403795_15405616.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15406377_15408651.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15408720_15409091.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15409095_15410457.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15410597_15443917.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15444074_15444168.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15444210_15444705.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15444884_15445395.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15445816_15445924.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15446027_15848772.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15849244_15849358.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15849530_15850266.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ntLink_6/3/15850716_16070598.trinity.reads
CMD: touch sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff.ok
CMD: /usr/local/bin/util/support_scripts//extract_reads_per_partition.pl --partitions_gff sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff  --coord_sorted_SAM sorted-bams-merged.bam.norm_200.bam.-.sam --parts_per_directory 100 --min_reads_per_partition 10  --SS_lib_type RF 
// parsing paritions.

[100]  
[200]  
[300]  
[400]  
[500]  
[600]  
[700]  
[800]  
[900]  
[1000]  
[1100]  
[1200]  
[1300]  
[1400]  
[1500]  
[1600]  
[1700]  
[1800]  
[1900]  
[2000]  
[2100]  
[2200]  
[2300]  
[2400]  
[2500]  
[2600]  
[2700]  
[2800]  
[2900]  
[3000]  
[3100]  
[3200]  
[3300]  
[3400]  
[3500]  
[3600]  
[3700]  
[3800]  
[3900]  
[4000]  
[4100]  
[4200]  
[4300]  
[4400]  
[4500]  
[4600]  
[4700]  
[4800]  
[4900]  
[5000]  
[5100]  
[5200]  
[5300]  
[5400]  
[5500]  
[5600]  
[5700]  
[5800]  
[5900]  
[6000]  
[6100]  
[6200]  
[6300]  
[6400]  
[6500]  
[6600]  
[6700]  
[6800]  
[6900]  
[7000]  
[7100]  
[7200]  
[7300]  
[7400]  
[7500]  
[7600]  
[7700]  
[7800]  
[7900]  
[8000]  
[8100]  
[8200]  
[8300]  
[8400]  
[8500]  
[8600]  
[8700]  
[8800]  
[8900]  
[9000]  
[9100]  
[9200]  
[9300]  
[9400]  
[9500]  
[9600]  
[9700]  
[9800]  
[9900]  
[10000]  
[10100]  
[10200]  
[10300]  
[10400]  
[10500]  
[10600]  
[10700]  
[10800]  
[10900]  
[11000]  
[11100]  
[11200]  
[11300]  
[11400]  
[11500]  
[11600]  
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[23840]  -writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ntLink_7/0/290_424.trinity.reads
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-writing to Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff/ptg000187l/0/17591_17972.trinity.reads
CMD: touch Dir_sorted-bams-merged.bam.norm_200.bam.+.sam.minC1.gff.ok
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-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000185l/0/27063_27992.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000185l/0/28133_28153.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000185l/0/32445_33180.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/56_483.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/786_1333.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/1527_1657.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/5656_5834.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/11638_11835.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/13984_18628.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/18847_18961.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/19562_19696.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/20576_20728.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/21871_22005.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/23191_23346.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/23356_23833.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/25673_26550.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/27130_27262.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/27593_27747.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/27803_27937.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/28052_28217.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/28249_28383.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000186l/0/28947_29089.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/1740_1895.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/1905_2382.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/4222_5099.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/5679_5811.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/6352_6486.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/6601_6766.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/6798_6932.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/7496_7890.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/8225_9434.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/9852_10896.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/11367_11653.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/11747_12132.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/13073_13583.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/14101_14235.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/14333_14467.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/15085_15333.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/15590_16148.trinity.reads
-writing to Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff/ptg000187l/0/16855_16989.trinity.reads
CMD: touch Dir_sorted-bams-merged.bam.norm_200.bam.-.sam.minC1.gff.ok
##
Done
##

Thursday, December 18, 2025: 15:54:31	CMD: touch partitions.ok
Thursday, December 18, 2025: 15:54:31	CMD: find Dir_* -name '*reads' > read_files.list
Thursday, December 18, 2025: 15:54:31	CMD: touch read_files.list.ok
Thursday, December 18, 2025: 15:54:31	CMD: /usr/local/bin/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  > trinity_GG.cmds
Thursday, December 18, 2025: 15:54:31	CMD: touch trinity_GG.cmds.ok
Thursday, December 18, 2025: 15:54:31	CMD: touch trinity_GG.cmds.ok


--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
--------------------------------------------------------------------------------

Thursday, December 18, 2025: 15:54:31	CMD: /usr/local/bin/trinity-plugins/BIN/ParaFly -c trinity_GG.cmds -CPU 44 -v -shuffle 
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All commands completed successfully. :-)

Friday, December 19, 2025: 02:40:20	CMD: find Dir_*  -name '*inity.fasta'  | /usr/local/bin/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/Trinity-GG.fasta.tmp
Friday, December 19, 2025: 02:40:22	CMD: mv /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir/Trinity-GG.fasta /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir.Trinity-GG.fasta
Friday, December 19, 2025: 02:40:39	CMD: /usr/local/bin/util/support_scripts/get_Trinity_gene_to_trans_map.pl /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir.Trinity-GG.fasta > /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir.Trinity-GG.fasta.gene_trans_map


Finished. See /home/shared/8TB_HDD_03/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/code/../output/00.30-D-Apul-transcriptome-assembly-Trinity/genome_guided_assembly/trinity_out_dir.Trinity-GG.fasta for reconstructed transcripts