Processing paired-end Bismark output file(s) (SAM format): 105M_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>105M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 105M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 105M_1_bismark_bt2_pe.bam: 4864 Total number duplicated alignments removed: 290 (5.96%) Duplicated alignments were found at: 264 different position(s) Total count of deduplicated leftover sequences: 4574 (94.04% of total) Processing paired-end Bismark output file(s) (SAM format): 105M_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>105M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Captured error message: '[main_samview] fail to read the header from "105M_1_bismark_bt2_pe.deduplicated.bam".' [ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting... Processing paired-end Bismark output file(s) (SAM format): 105M_1_bismark_bt2_pe.deduplicated.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>105M_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... Captured error message: '[main_samview] fail to read the header from "105M_1_bismark_bt2_pe.deduplicated.deduplicated.bam".' [ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting... Processing paired-end Bismark output file(s) (SAM format): 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.deduplicated.bam Total number of alignments analysed in 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam: 4574 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4574 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.deduplicated.deduplicated.bam Total number of alignments analysed in 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.deduplicated.bam: 4574 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4574 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 106M_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>106M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 106M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 106M_1_bismark_bt2_pe.bam: 4749 Total number duplicated alignments removed: 374 (7.88%) Duplicated alignments were found at: 336 different position(s) Total count of deduplicated leftover sequences: 4375 (92.12% of total) Processing paired-end Bismark output file(s) (SAM format): 106M_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>106M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 106M_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in 106M_1_bismark_bt2_pe.deduplicated.bam: 4375 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4375 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 107M_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>107M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 107M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 107M_1_bismark_bt2_pe.bam: 4683 Total number duplicated alignments removed: 330 (7.05%) Duplicated alignments were found at: 300 different position(s) Total count of deduplicated leftover sequences: 4353 (92.95% of total) Processing paired-end Bismark output file(s) (SAM format): 107M_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>107M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 107M_1_bismark_bt2_pe.deduplicated.deduplicated.bam [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes samtools view: error reading file "107M_1_bismark_bt2_pe.deduplicated.bam" samtools view: error closing "107M_1_bismark_bt2_pe.deduplicated.bam": -1 Total number of alignments analysed in 107M_1_bismark_bt2_pe.deduplicated.bam: 4246 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4246 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 107M_1_bismark_bt2_pe.deduplicated.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>107M_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam Total number of alignments analysed in 107M_1_bismark_bt2_pe.deduplicated.deduplicated.bam: 4353 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4353 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.deduplicated.bam [main_samview] fail to read the header from "107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam". Total number of alignments analysed in 107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam: 0 Total number duplicated alignments removed: 0 (N/A%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 0 (N/A% of total) [main_samview] fail to read the header from "-". Failed to close output filehandle: Processing paired-end Bismark output file(s) (SAM format): 239M_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>239M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 239M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 239M_1_bismark_bt2_pe.bam: 4744 Total number duplicated alignments removed: 315 (6.64%) Duplicated alignments were found at: 284 different position(s) Total count of deduplicated leftover sequences: 4429 (93.36% of total) Processing paired-end Bismark output file(s) (SAM format): 239M_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>239M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 239M_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in 239M_1_bismark_bt2_pe.deduplicated.bam: 4429 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4429 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 270M_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>270M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 270M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 270M_1_bismark_bt2_pe.bam: 4693 Total number duplicated alignments removed: 355 (7.56%) Duplicated alignments were found at: 326 different position(s) Total count of deduplicated leftover sequences: 4338 (92.44% of total) Processing paired-end Bismark output file(s) (SAM format): 270M_1_bismark_bt2_pe.deduplicated.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>270M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 270M_1_bismark_bt2_pe.deduplicated.deduplicated.bam [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes samtools view: error reading file "270M_1_bismark_bt2_pe.deduplicated.bam" samtools view: error closing "270M_1_bismark_bt2_pe.deduplicated.bam": -1 Total number of alignments analysed in 270M_1_bismark_bt2_pe.deduplicated.bam: 3564 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 3564 (100.00% of total) *** Bismark methylation extractor version v0.24.2 *** Trying to determine the type of mapping from the SAM header line of file 105M_1_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Core usage currently set to more than 20 threads. Let's see how this goes... (set value: 28) Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 28 Strand-specific outputs will be skipped. Separate output files for cytosines in CpG, CHG and CHH context will be generated Merge CHG and CHH context to non-CpG context specified Output will be written to the current directory ('/mmfs1/gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/04-bismark-pipeline') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>105M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...passed! Writing result file containing methylation information for C in CpG context to CpG_context_105M_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in any other context to Non_CpG_context_105M_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 105M_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_086373.1 LN:113486924 skipping SAM header line: @SQ SN:NC_086374.1 LN:103707636 skipping SAM header line: @SQ SN:NC_086375.1 LN:94312406 skipping SAM header line: @SQ SN:NC_086376.1 LN:96324366 skipping SAM header line: @SQ SN:NC_086377.1 LN:88129055 skipping SAM header line: @SQ SN:NC_086378.1 LN:91445414 skipping SAM header line: @SQ SN:NC_086379.1 LN:85406108 skipping SAM header line: @SQ SN:NC_086380.1 LN:80675551 skipping SAM header line: @SQ SN:NC_086381.1 LN:82295107 skipping SAM header line: @SQ SN:NC_086382.1 LN:78455819 skipping SAM header line: @SQ SN:NC_086383.1 LN:71253669 skipping SAM header line: @SQ SN:NC_086384.1 LN:60198110 skipping SAM header line: @SQ SN:NC_086385.1 LN:63222996 skipping SAM header line: @SQ SN:NC_086386.1 LN:81773519 skipping SAM header line: @SQ SN:NW_026963290.1 LN:8139973 skipping SAM header line: @SQ SN:NW_026963291.1 LN:22515 skipping SAM header line: @SQ SN:NW_026963292.1 LN:5553665 skipping SAM header line: @SQ SN:NW_026963293.1 LN:500000 skipping SAM header line: @SQ SN:NW_026963294.1 LN:5965364 skipping SAM header line: @SQ SN:NW_026963295.1 LN:6074899 skipping SAM header line: @SQ SN:NW_026963296.1 LN:3628579 skipping SAM header line: @SQ SN:NW_026963297.1 LN:3444836 skipping SAM header line: @SQ SN:NW_026963298.1 LN:2989614 skipping SAM header line: @SQ SN:NW_026963299.1 LN:250000 skipping SAM header line: @SQ SN:NW_026963300.1 LN:356632 skipping SAM header line: @SQ SN:NW_026963301.1 LN:4334515 skipping SAM header line: @SQ SN:NW_026963302.1 LN:4076163 skipping SAM header line: @SQ SN:NW_026963303.1 LN:250000 skipping SAM header line: @SQ SN:NW_026963304.1 LN:4603332 skipping SAM header line: @SQ SN:NW_026963305.1 LN:1250000 skipping SAM header line: @SQ SN:NW_026963306.1 LN:121029 skipping SAM header line: @SQ SN:NW_026963307.1 LN:125000 skipping SAM header line: @SQ SN:NW_026963308.1 LN:418548 skipping SAM header line: @SQ SN:NW_026963309.1 LN:710015 skipping SAM header line: @SQ SN:NW_026963310.1 LN:3670610 skipping SAM header line: @SQ SN:NW_026963311.1 LN:1420456 skipping SAM header line: @SQ SN:NW_026963312.1 LN:1013396 skipping SAM header line: @SQ SN:NW_026963313.1 LN:825963 skipping SAM header line: @SQ SN:NW_026963314.1 LN:2737876 skipping SAM header line: @SQ SN:NW_026963315.1 LN:4066460 skipping SAM header line: @SQ SN:NW_026963316.1 LN:450949 skipping SAM header line: @SQ SN:NW_026963317.1 LN:4467411 skipping SAM header line: @SQ SN:NW_026963318.1 LN:3454087 skipping SAM header line: @SQ SN:NW_026963319.1 LN:250000 skipping SAM header line: @SQ SN:NW_026963320.1 LN:175774 skipping SAM header line: @SQ SN:NW_026963321.1 LN:741490 skipping SAM header line: @SQ SN:NW_026963322.1 LN:899002 skipping SAM header line: @SQ SN:NW_026963323.1 LN:961498 skipping SAM header line: @SQ SN:NW_026963324.1 LN:293216 skipping SAM header line: @SQ SN:NW_026963325.1 LN:26743 skipping SAM header line: @SQ SN:NW_026963326.1 LN:30845 skipping SAM header line: @SQ SN:NW_026963327.1 LN:35643 skipping SAM header line: @SQ SN:NW_026963328.1 LN:31473 skipping SAM header line: @SQ SN:NW_026963329.1 LN:267817 skipping SAM header line: @SQ SN:NW_026963330.1 LN:38397 skipping SAM header line: @SQ SN:NW_026963331.1 LN:73781 skipping SAM header line: @SQ SN:NW_026963332.1 LN:1260917 skipping SAM header line: @SQ SN:NW_026963333.1 LN:250000 skipping SAM header line: @SQ SN:NW_026963334.1 LN:25388 skipping SAM header line: @SQ SN:NW_026963335.1 LN:565390 skipping SAM header line: @SQ SN:NW_026963336.1 LN:26109 skipping SAM header line: @SQ SN:NW_026963337.1 LN:659095 skipping SAM header line: @SQ SN:NW_026963338.1 LN:357655 skipping SAM header line: @SQ SN:NW_026963339.1 LN:277346 skipping SAM header line: @SQ SN:NW_026963340.1 LN:4220937 skipping SAM header line: @SQ SN:NW_026963341.1 LN:122847 skipping SAM header line: @SQ SN:NW_026963342.1 LN:58283 skipping SAM header line: @SQ SN:NW_026963343.1 LN:556242 skipping SAM header line: @SQ SN:NW_026963344.1 LN:203489 skipping SAM header line: @SQ SN:NW_026963345.1 LN:224476 skipping SAM header line: @SQ SN:NW_026963346.1 LN:651063 skipping SAM header line: @SQ SN:NW_026963347.1 LN:1227606 skipping SAM header line: @SQ SN:NW_026963348.1 LN:21803 skipping SAM header line: @SQ SN:NW_026963349.1 LN:40271 skipping SAM header line: @SQ SN:NW_026963350.1 LN:1415666 skipping SAM header line: @SQ SN:NW_026963351.1 LN:17622 skipping SAM header line: @SQ SN:NW_026963352.1 LN:337009 skipping SAM header line: @SQ SN:NW_026963353.1 LN:20381 skipping SAM header line: @SQ SN:NW_026963354.1 LN:394918 skipping SAM header line: @SQ SN:NW_026963355.1 LN:24539 skipping SAM header line: @SQ SN:NW_026963356.1 LN:34117 skipping SAM header line: @SQ SN:NW_026963357.1 LN:666514 skipping SAM header line: @SQ SN:NW_026963358.1 LN:27938 skipping SAM header line: @SQ SN:NW_026963359.1 LN:23142 skipping SAM header line: @SQ SN:NW_026963360.1 LN:21876 skipping SAM header line: @SQ SN:NW_026963361.1 LN:21893 skipping SAM header line: @SQ SN:NW_026963362.1 LN:29136 skipping SAM header line: @SQ SN:NW_026963363.1 LN:419011 skipping SAM header line: @SQ SN:NW_026963364.1 LN:60149 skipping SAM header line: @SQ SN:NW_026963365.1 LN:61440 skipping SAM header line: @SQ SN:NW_026963366.1 LN:26902 skipping SAM header line: @SQ SN:NW_026963367.1 LN:51097 skipping SAM header line: @SQ SN:NW_026963368.1 LN:77113 skipping SAM header line: @SQ SN:NW_026963369.1 LN:121069 skipping SAM header line: @SQ SN:NW_026963370.1 LN:866335 skipping SAM header line: @SQ SN:NW_026963371.1 LN:332943 skipping SAM header line: @SQ SN:NW_026963372.1 LN:501245 skipping SAM header line: @SQ SN:NW_026963373.1 LN:41944 skipping SAM header line: @SQ SN:NW_026963374.1 LN:73985 skipping SAM header line: @SQ SN:NW_026963375.1 LN:53741 skipping SAM header line: @SQ SN:NW_026963376.1 LN:53927 skipping SAM header line: @SQ SN:NW_026963377.1 LN:15328 skipping SAM header line: @SQ SN:NW_026963378.1 LN:612846 skipping SAM header line: @SQ SN:NW_026963379.1 LN:30276 skipping SAM header line: @SQ SN:NW_026963380.1 LN:20427 skipping SAM header line: @SQ SN:NW_026963381.1 LN:25540 skipping SAM header line: @SQ SN:NW_026963382.1 LN:58265 skipping SAM header line: @SQ SN:NW_026963383.1 LN:25711 skipping SAM header line: @SQ SN:NW_026963384.1 LN:18896 skipping SAM header line: @SQ SN:NW_026963385.1 LN:34901 skipping SAM header line: @SQ SN:NW_026963386.1 LN:25234 skipping SAM header line: @SQ SN:NW_026963387.1 LN:66105 skipping SAM header line: @SQ SN:NW_026963388.1 LN:30312 skipping SAM header line: @SQ SN:NW_026963389.1 LN:32428 skipping SAM header line: @SQ SN:NW_026963390.1 LN:25381 skipping SAM header line: @SQ SN:NW_026963391.1 LN:26017 skipping SAM header line: @SQ SN:NW_026963392.1 LN:25685 skipping SAM header line: @SQ SN:NW_026963393.1 LN:19274 skipping SAM header line: @SQ SN:NW_026963394.1 LN:27950 skipping SAM header line: @SQ SN:NW_026963395.1 LN:45255 skipping SAM header line: @SQ SN:NW_026963396.1 LN:63704 skipping SAM header line: @SQ SN:NW_026963397.1 LN:22806 skipping SAM header line: @SQ SN:NW_026963398.1 LN:24645 skipping SAM header line: @SQ SN:NW_026963399.1 LN:50812 skipping SAM header line: @SQ SN:NW_026963400.1 LN:70378 skipping SAM header line: @SQ SN:NW_026963401.1 LN:21165 skipping SAM header line: @SQ SN:NW_026963402.1 LN:95337 skipping SAM header line: @SQ SN:NW_026963403.1 LN:32744 skipping SAM header line: @SQ SN:NW_026963404.1 LN:32390 skipping SAM header line: @SQ SN:NW_026963405.1 LN:20760 skipping SAM header line: @SQ SN:NW_026963406.1 LN:17091 skipping SAM header line: @SQ SN:NW_026963407.1 LN:25441 skipping SAM header line: @SQ SN:NW_026963408.1 LN:32110 skipping SAM header line: @SQ SN:NW_026963409.1 LN:25245 skipping SAM header line: @SQ SN:NW_026963410.1 LN:26685 skipping SAM header line: @SQ SN:NW_026963411.1 LN:26243 skipping SAM header line: @SQ SN:NW_026963412.1 LN:23891 skipping SAM header line: @SQ SN:NW_026963413.1 LN:32257 skipping SAM header line: @SQ SN:NW_026963414.1 LN:35770 skipping SAM header line: @SQ SN:NW_026963415.1 LN:28815 skipping SAM header line: @SQ SN:NW_026963416.1 LN:33904 skipping SAM header line: @SQ SN:NW_026963417.1 LN:59749 skipping SAM header line: @SQ SN:NW_026963418.1 LN:81418 skipping SAM header line: @SQ SN:NW_026963419.1 LN:107657 skipping SAM header line: @SQ SN:NW_026963420.1 LN:30761 skipping SAM header line: @SQ SN:NW_026963421.1 LN:23947 skipping SAM header line: @SQ SN:NW_026963422.1 LN:18164 skipping SAM header line: @SQ SN:NW_026963423.1 LN:25693 skipping SAM header line: @SQ SN:NW_026963424.1 LN:91214 skipping SAM header line: @SQ SN:NW_026963425.1 LN:28588 skipping SAM header line: @SQ SN:NW_026963426.1 LN:22706 skipping SAM header line: @SQ SN:NW_026963427.1 LN:31282 skipping SAM header line: @SQ SN:NW_026963428.1 LN:29918 skipping SAM header line: @SQ SN:NW_026963429.1 LN:18537 skipping SAM header line: @SQ SN:NW_026963430.1 LN:19656 skipping SAM header line: @SQ SN:NW_026963431.1 LN:24459 skipping SAM header line: @SQ SN:NW_026963432.1 LN:22327 skipping SAM header line: @SQ SN:NW_026963433.1 LN:105369 skipping SAM header line: @SQ SN:NW_026963434.1 LN:26908 skipping SAM header line: @SQ SN:NW_026963435.1 LN:28497 skipping SAM header line: @SQ SN:NW_026963436.1 LN:36282 skipping SAM header line: @SQ SN:NW_026963437.1 LN:23739 skipping SAM header line: @SQ SN:NW_026963438.1 LN:24630 skipping SAM header line: @SQ SN:NW_026963439.1 LN:34452 skipping SAM header line: @SQ SN:NW_026963440.1 LN:33196 skipping SAM header line: @SQ SN:NW_026963441.1 LN:21370 skipping SAM header line: @SQ SN:NW_026963442.1 LN:20837 skipping SAM header line: @SQ SN:NW_026963443.1 LN:56464 skipping SAM header line: @SQ SN:NW_026963444.1 LN:22596 skipping SAM header line: @SQ SN:NW_026963445.1 LN:89992 skipping SAM header line: @SQ SN:NW_026963446.1 LN:20471 skipping SAM header line: @SQ SN:NW_026963447.1 LN:25005 skipping SAM header line: @SQ SN:NW_026963448.1 LN:22800 skipping SAM header line: @SQ SN:NW_026963449.1 LN:48946 skipping SAM header line: @SQ SN:NW_026963450.1 LN:23621 skipping SAM header line: @SQ SN:NW_026963451.1 LN:69983 skipping SAM header line: @SQ SN:NW_026963452.1 LN:26246 skipping SAM header line: @SQ SN:NW_026963453.1 LN:73232 skipping SAM header line: @SQ SN:NW_026963454.1 LN:23625 skipping SAM header line: @SQ SN:NW_026963455.1 LN:21431 skipping SAM header line: @SQ SN:NW_026963456.1 LN:20408 skipping SAM header line: @SQ SN:NW_026963457.1 LN:23150 skipping SAM header line: @SQ SN:NW_026963458.1 LN:20814 skipping SAM header line: @SQ SN:NW_026963459.1 LN:33799 skipping SAM header line: @SQ SN:NW_026963460.1 LN:22951 skipping SAM header line: @SQ SN:NW_026963461.1 LN:39207 skipping SAM header line: @SQ SN:NW_026963462.1 LN:16320 skipping SAM header line: @SQ SN:NW_026963463.1 LN:19723 skipping SAM header line: @SQ SN:NW_026963464.1 LN:19884 skipping SAM header line: @SQ SN:NW_026963465.1 LN:17047 skipping SAM header line: @SQ SN:NW_026963466.1 LN:28987 skipping SAM header line: @SQ SN:NW_026963467.1 LN:26703 skipping SAM header line: @SQ SN:NW_026963468.1 LN:27006 skipping SAM header line: @SQ SN:NW_026963469.1 LN:21377 skipping SAM header line: @SQ SN:NW_026963470.1 LN:31960 skipping SAM header line: @SQ SN:NW_026963471.1 LN:89899 skipping SAM header line: @SQ SN:NW_026963472.1 LN:52362 skipping SAM header line: @SQ SN:NW_026963473.1 LN:46928 skipping SAM header line: @SQ SN:NW_026963474.1 LN:24695 skipping SAM header line: @SQ SN:NW_026963475.1 LN:38188 skipping SAM header line: @SQ SN:NW_026963476.1 LN:22631 skipping SAM header line: @SQ SN:NW_026963477.1 LN:17795 skipping SAM header line: @SQ SN:NW_026963478.1 LN:20901 skipping SAM header line: @SQ SN:NW_026963479.1 LN:26325 skipping SAM header line: @SQ SN:NW_026963480.1 LN:22825 skipping SAM header line: @SQ SN:NW_026963481.1 LN:23040 skipping SAM header line: @SQ SN:NW_026963482.1 LN:21352 skipping SAM header line: @SQ SN:NW_026963483.1 LN:19517 skipping SAM header line: @SQ SN:NW_026963484.1 LN:43699 skipping SAM header line: @SQ SN:NW_026963485.1 LN:14016 skipping SAM header line: @SQ SN:NW_026963486.1 LN:13954 skipping SAM header line: @SQ SN:NW_026963487.1 LN:25855 skipping SAM header line: @SQ SN:NW_026963488.1 LN:21550 skipping SAM header line: @SQ SN:NW_026963489.1 LN:33800 skipping SAM header line: @SQ SN:NW_026963490.1 LN:20306 skipping SAM header line: @SQ SN:NW_026963491.1 LN:32733 skipping SAM header line: @SQ SN:NW_026963492.1 LN:41996 skipping SAM header line: @SQ SN:NW_026963493.1 LN:27834 skipping SAM header line: @SQ SN:NW_026963494.1 LN:23165 skipping SAM header line: @SQ SN:NW_026963495.1 LN:21648 skipping SAM header line: @SQ SN:NW_026963496.1 LN:27514 skipping SAM header line: @SQ SN:NW_026963497.1 LN:22988 skipping SAM header line: @SQ SN:NW_026963498.1 LN:27759 skipping SAM header line: @SQ SN:NW_026963499.1 LN:31922 skipping SAM header line: @SQ SN:NW_026963500.1 LN:55274 skipping SAM header line: @SQ SN:NW_026963501.1 LN:19548 skipping SAM header line: @SQ SN:NW_026963502.1 LN:19545 skipping SAM header line: @SQ SN:NW_026963503.1 LN:31769 skipping SAM header line: @SQ SN:NW_026963504.1 LN:20921 skipping SAM header line: @SQ SN:NW_026963505.1 LN:26440 skipping SAM header line: @SQ SN:NW_026963506.1 LN:36130 skipping SAM header line: @SQ SN:NW_026963507.1 LN:50233 skipping SAM header line: @SQ SN:NW_026963508.1 LN:37121 skipping SAM header line: @SQ SN:NW_026963509.1 LN:15802 skipping SAM header line: @SQ SN:NW_026963510.1 LN:21446 skipping SAM header line: @SQ SN:NW_026963511.1 LN:16917 skipping SAM header line: @SQ SN:NW_026963512.1 LN:24391 skipping SAM header line: @SQ SN:NW_026963513.1 LN:19462 skipping SAM header line: @SQ SN:NW_026963514.1 LN:24066 skipping SAM header line: @SQ SN:NW_026963515.1 LN:17459 skipping SAM header line: @SQ SN:NW_026963516.1 LN:18652 skipping SAM header line: @SQ SN:NW_026963517.1 LN:8618 skipping SAM header line: @SQ SN:NW_026963518.1 LN:20873 skipping SAM header line: @SQ SN:NW_026963519.1 LN:32632 skipping SAM header line: @SQ SN:NW_026963520.1 LN:36645 skipping SAM header line: @SQ SN:NW_026963521.1 LN:23952 skipping SAM header line: @SQ SN:NW_026963522.1 LN:22556 skipping SAM header line: @SQ SN:NW_026963523.1 LN:15718 skipping SAM header line: @SQ SN:NW_026963524.1 LN:50340 skipping SAM header line: @SQ SN:NW_026963525.1 LN:23212 skipping SAM header line: @SQ SN:NW_026963526.1 LN:18080 skipping SAM header line: @SQ SN:NW_026963527.1 LN:24976 skipping SAM header line: @SQ SN:NW_026963528.1 LN:20932 skipping SAM header line: @SQ SN:NW_026963529.1 LN:20070 skipping SAM header line: @SQ SN:NW_026963530.1 LN:43040 skipping SAM header line: @SQ SN:NW_026963531.1 LN:22373 skipping SAM header line: @SQ SN:NW_026963532.1 LN:21610 skipping SAM header line: @SQ SN:NW_026963533.1 LN:25225 skipping SAM header line: @SQ SN:NW_026963534.1 LN:22597 skipping SAM header line: @SQ SN:NW_026963535.1 LN:18239 skipping SAM header line: @SQ SN:NW_026963536.1 LN:19511 skipping SAM header line: @SQ SN:NW_026963537.1 LN:25744 skipping SAM header line: @SQ SN:NW_026963538.1 LN:33248 skipping SAM header line: @SQ SN:NW_026963539.1 LN:16194 skipping SAM header line: @SQ SN:NW_026963540.1 LN:29982 skipping SAM header line: @SQ SN:NW_026963541.1 LN:38121 skipping SAM header line: @SQ SN:NW_026963542.1 LN:23886 skipping SAM header line: @SQ SN:NW_026963543.1 LN:22120 skipping SAM header line: @SQ SN:NW_026963544.1 LN:40706 skipping SAM header line: @SQ SN:NW_026963545.1 LN:22511 skipping SAM header line: @SQ SN:NW_026963546.1 LN:29792 skipping SAM header line: @SQ SN:NW_026963547.1 LN:15422 skipping SAM header line: @SQ SN:NW_026963548.1 LN:28602 skipping SAM header line: @SQ SN:NW_026963549.1 LN:29363 skipping SAM header line: @SQ SN:NW_026963550.1 LN:42899 skipping SAM header line: @SQ SN:NW_026963551.1 LN:28569 skipping SAM header line: @SQ SN:NW_026963552.1 LN:47249 skipping SAM header line: @SQ SN:NW_026963553.1 LN:40295 skipping SAM header line: @SQ SN:NW_026963554.1 LN:23298 skipping SAM header line: @SQ SN:NW_026963555.1 LN:17778 skipping SAM header line: @SQ SN:NW_026963556.1 LN:40663 skipping SAM header line: @SQ SN:NW_026963557.1 LN:19240 skipping SAM header line: @SQ SN:NW_026963558.1 LN:53464 skipping SAM header line: @SQ SN:NW_026963559.1 LN:20496 skipping SAM header line: @SQ SN:NW_026963560.1 LN:18775 skipping SAM header line: @SQ SN:NW_026963561.1 LN:22720 skipping SAM header line: @SQ SN:NW_026963562.1 LN:29987 skipping SAM header line: @SQ SN:NW_026963563.1 LN:17061 skipping SAM header line: @SQ SN:NW_026963564.1 LN:19136 skipping SAM header line: @SQ SN:NW_026963565.1 LN:18594 skipping SAM header line: @SQ SN:NW_026963566.1 LN:21889 skipping SAM header line: @SQ SN:NW_026963567.1 LN:42002 skipping SAM header line: @SQ SN:NW_026963568.1 LN:28438 skipping SAM header line: @SQ SN:NW_026963569.1 LN:27574 skipping SAM header line: @SQ SN:NW_026963570.1 LN:26209 skipping SAM header line: @SQ SN:NW_026963571.1 LN:32307 skipping SAM header line: @SQ SN:NW_026963572.1 LN:23566 skipping SAM header line: @SQ SN:NW_026963573.1 LN:20539 skipping SAM header line: @SQ SN:NW_026963574.1 LN:19425 skipping SAM header line: @SQ SN:NW_026963575.1 LN:32111 skipping SAM header line: @SQ SN:NW_026963576.1 LN:34506 skipping SAM header line: @SQ SN:NW_026963577.1 LN:20176 skipping SAM header line: @SQ SN:NW_026963578.1 LN:24377 skipping SAM header line: @SQ SN:NW_026963579.1 LN:55969 skipping SAM header line: @SQ SN:NW_026963580.1 LN:27671 skipping SAM header line: @SQ SN:NW_026963581.1 LN:24138 skipping SAM header line: @SQ SN:NW_026963582.1 LN:97536 skipping SAM header line: @SQ SN:NW_026963583.1 LN:63607 skipping SAM header line: @SQ SN:NW_026963584.1 LN:34460 skipping SAM header line: @SQ SN:NW_026963585.1 LN:49376 skipping SAM header line: @SQ SN:NW_026963586.1 LN:27685 skipping SAM header line: @SQ SN:NW_026963587.1 LN:24514 skipping SAM header line: @SQ SN:NW_026963588.1 LN:48354 skipping SAM header line: @SQ SN:NW_026963589.1 LN:26316 skipping SAM header line: @SQ SN:NW_026963590.1 LN:22686 skipping SAM header line: @SQ SN:NW_026963591.1 LN:23266 skipping SAM header line: @SQ SN:NW_026963592.1 LN:19131 skipping SAM header line: @SQ SN:NW_026963593.1 LN:17046 skipping SAM header line: @SQ SN:NW_026963594.1 LN:23204 skipping SAM header line: @SQ SN:NW_026963595.1 LN:23624 skipping SAM header line: @SQ SN:NW_026963596.1 LN:19410 skipping SAM header line: @SQ SN:NW_026963597.1 LN:4560 skipping SAM header line: @SQ SN:NW_026963598.1 LN:29441 skipping SAM header line: @SQ SN:NW_026963599.1 LN:40152 skipping SAM header line: @SQ SN:NW_026963600.1 LN:21122 skipping SAM header line: @SQ SN:NW_026963601.1 LN:36140 skipping SAM header line: @SQ SN:NW_026963602.1 LN:18515 skipping SAM header line: @SQ SN:NW_026963603.1 LN:20142 skipping SAM header line: @SQ SN:NW_026963604.1 LN:25383 skipping SAM header line: @SQ SN:NW_026963605.1 LN:28494 skipping SAM header line: @SQ SN:NW_026963606.1 LN:18177 skipping SAM header line: @SQ SN:NW_026963607.1 LN:18627 skipping SAM header line: @SQ SN:NW_026963608.1 LN:22139 skipping SAM header line: @SQ SN:NW_026963609.1 LN:25457 skipping SAM header line: @SQ SN:NW_026963610.1 LN:20696 skipping SAM header line: @SQ SN:NW_026963611.1 LN:20121 skipping SAM header line: @SQ SN:NW_026963612.1 LN:23855 skipping SAM header line: @SQ SN:NW_026963613.1 LN:19683 skipping SAM header line: @SQ SN:NW_026963614.1 LN:17735 skipping SAM header line: @SQ SN:NW_026963615.1 LN:24639 skipping SAM header line: @SQ SN:NW_026963616.1 LN:36520 skipping SAM header line: @SQ SN:NW_026963617.1 LN:29370 skipping SAM header line: @SQ SN:NW_026963618.1 LN:25732 skipping SAM header line: @SQ SN:NW_026963619.1 LN:23735 skipping SAM header line: @SQ SN:NW_026963620.1 LN:21397 skipping SAM header line: @SQ SN:NW_026963621.1 LN:21572 skipping SAM header line: @SQ SN:NW_026963622.1 LN:25321 skipping SAM header line: @SQ SN:NW_026963623.1 LN:18363 skipping SAM header line: @SQ SN:NW_026963624.1 LN:20416 skipping SAM header line: @SQ SN:NW_026963625.1 LN:20064 skipping SAM header line: @SQ SN:NW_026963626.1 LN:37124 skipping SAM header line: @SQ SN:NW_026963627.1 LN:23433 skipping SAM header line: @SQ SN:NW_026963628.1 LN:24267 skipping SAM header line: @SQ SN:NW_026963629.1 LN:25181 skipping SAM header line: @SQ SN:NW_026963630.1 LN:20211 skipping SAM header line: @SQ SN:NW_026963631.1 LN:26376 skipping SAM header line: @SQ SN:NW_026963632.1 LN:20626 skipping SAM header line: @SQ SN:NW_026963633.1 LN:32619 skipping SAM header line: @SQ SN:NW_026963634.1 LN:21163 skipping SAM header line: @SQ SN:NW_026963635.1 LN:18606 skipping SAM header line: @SQ SN:NW_026963636.1 LN:18842 skipping SAM header line: @SQ SN:NW_026963637.1 LN:25787 skipping SAM header line: @SQ SN:NW_026963638.1 LN:21305 skipping SAM header line: @SQ SN:NW_026963639.1 LN:24239 skipping SAM header line: @SQ SN:NW_026963640.1 LN:24465 skipping SAM header line: @SQ SN:NW_026963641.1 LN:26936 skipping SAM header line: @SQ SN:NW_026963642.1 LN:22173 skipping SAM header line: @SQ SN:NW_026963643.1 LN:33930 skipping SAM header line: @SQ SN:NW_026963644.1 LN:30601 skipping SAM header line: @SQ SN:NW_026963645.1 LN:27131 skipping SAM header line: @SQ SN:NW_026963646.1 LN:21725 skipping SAM header line: @SQ SN:NW_026963647.1 LN:17559 skipping SAM header line: @SQ SN:NW_026963648.1 LN:26423 skipping SAM header line: @SQ SN:NW_026963649.1 LN:23991 skipping SAM header line: @SQ SN:NW_026963650.1 LN:21075 skipping SAM header line: @SQ SN:NW_026963651.1 LN:37035 skipping SAM header line: @SQ SN:NW_026963652.1 LN:20328 skipping SAM header line: @SQ SN:NW_026963653.1 LN:17920 skipping SAM header line: @SQ SN:NW_026963654.1 LN:25257 skipping SAM header line: @SQ SN:NW_026963655.1 LN:21611 skipping SAM header line: @SQ SN:NW_026963656.1 LN:31880 skipping SAM header line: @SQ SN:NW_026963657.1 LN:17971 skipping SAM header line: @SQ SN:NW_026963658.1 LN:17181 skipping SAM header line: @SQ SN:NW_026963659.1 LN:21841 skipping SAM header line: @SQ SN:NW_026963660.1 LN:48676 skipping SAM header line: @SQ SN:NW_026963661.1 LN:19775 skipping SAM header line: @SQ SN:NW_026963662.1 LN:35568 skipping SAM header line: @SQ SN:NW_026963663.1 LN:21947 skipping SAM header line: @SQ SN:NW_026963664.1 LN:24250 skipping SAM header line: @SQ SN:NW_026963665.1 LN:21491 skipping SAM header line: @SQ SN:NW_026963666.1 LN:22260 skipping SAM header line: @SQ SN:NW_026963667.1 LN:28403 skipping SAM header line: @SQ SN:NW_026963668.1 LN:19543 skipping SAM header line: @SQ SN:NW_026963669.1 LN:59060 skipping SAM header line: @SQ SN:NW_026963670.1 LN:23088 skipping SAM header line: @SQ SN:NW_026963671.1 LN:25210 skipping SAM header line: @SQ SN:NW_026963672.1 LN:29503 skipping SAM header line: @SQ SN:NW_026963673.1 LN:26257 skipping SAM header line: @SQ SN:NW_026963674.1 LN:22982 skipping SAM header line: @SQ SN:NW_026963675.1 LN:20127 skipping SAM header line: @SQ SN:NW_026963676.1 LN:21567 skipping SAM header line: @SQ SN:NW_026963677.1 LN:25240 skipping SAM header line: @SQ SN:NW_026963678.1 LN:25959 skipping SAM header line: @SQ SN:NW_026963679.1 LN:23464 skipping SAM header line: @SQ SN:NW_026963680.1 LN:23133 skipping SAM header line: @SQ SN:NW_026963681.1 LN:22873 skipping SAM header line: @SQ SN:NW_026963682.1 LN:27482 skipping SAM header line: @SQ SN:NW_026963683.1 LN:23835 skipping SAM header line: @SQ SN:NW_026963684.1 LN:18595 skipping SAM header line: @SQ SN:NW_026963685.1 LN:25677 skipping SAM header line: @SQ SN:NW_026963686.1 LN:25352 skipping SAM header line: @SQ SN:NW_026963687.1 LN:26654 skipping SAM header line: @SQ SN:NW_026963688.1 LN:16682 skipping SAM header line: @SQ SN:NW_026963689.1 LN:43634 skipping SAM header line: @SQ SN:NW_026963690.1 LN:20473 skipping SAM header line: @SQ SN:NW_026963691.1 LN:24782 skipping SAM header line: @SQ SN:NW_026963692.1 LN:27429 skipping SAM header line: @SQ SN:NW_026963693.1 LN:22023 skipping SAM header line: @SQ SN:NW_026963694.1 LN:22432 skipping SAM header line: @SQ SN:NW_026963695.1 LN:27801 skipping SAM header line: @SQ SN:NW_026963696.1 LN:89040 skipping SAM header line: @SQ SN:NW_026963697.1 LN:29127 skipping SAM header line: @SQ SN:NW_026963698.1 LN:22758 skipping SAM header line: @SQ SN:NW_026963699.1 LN:21265 skipping SAM header line: @SQ SN:NW_026963700.1 LN:32610 skipping SAM header line: @SQ SN:NW_026963701.1 LN:40879 skipping SAM header line: @SQ SN:NW_026963702.1 LN:25242 skipping SAM header line: @SQ SN:NW_026963703.1 LN:27008 skipping SAM header line: @SQ SN:NW_026963704.1 LN:21375 skipping SAM header line: @SQ SN:NW_026963705.1 LN:33180 skipping SAM header line: @SQ SN:NW_026963706.1 LN:26193 skipping SAM header line: @SQ SN:NW_026963707.1 LN:21669 skipping SAM header line: @SQ SN:NW_026963708.1 LN:25618 skipping SAM header line: @SQ SN:NW_026963709.1 LN:25056 skipping SAM header line: @SQ SN:NW_026963710.1 LN:22608 skipping SAM header line: @SQ SN:NW_026963711.1 LN:23115 skipping SAM header line: @SQ SN:NW_026963712.1 LN:22043 skipping SAM header line: @SQ SN:NW_026963713.1 LN:25891 skipping SAM header line: @SQ SN:NW_026963714.1 LN:24871 skipping SAM header line: @SQ SN:NW_026963715.1 LN:22811 skipping SAM header line: @SQ SN:NW_026963716.1 LN:38945 skipping SAM header line: @SQ SN:NW_026963717.1 LN:35514 skipping SAM header line: @SQ SN:NW_026963718.1 LN:21356 skipping SAM header line: @SQ SN:NW_026963719.1 LN:28341 skipping SAM header line: @SQ SN:NW_026963720.1 LN:20602 skipping SAM header line: @SQ SN:NW_026963721.1 LN:20995 skipping SAM header line: @SQ SN:NW_026963722.1 LN:21623 skipping SAM header line: @SQ SN:NW_026963723.1 LN:22869 skipping SAM header line: @SQ SN:NW_026963724.1 LN:22118 skipping SAM header line: @SQ SN:NW_026963725.1 LN:27787 skipping SAM header line: @SQ SN:NW_026963726.1 LN:28118 skipping SAM header line: @SQ SN:NW_026963727.1 LN:22374 skipping SAM header line: @SQ SN:NW_026963728.1 LN:26688 skipping SAM header line: @SQ SN:NW_026963729.1 LN:18680 skipping SAM header line: @SQ SN:NW_026963730.1 LN:26877 skipping SAM header line: @SQ SN:NW_026963731.1 LN:22152 skipping SAM header line: @SQ SN:NW_026963732.1 LN:21122 skipping SAM header line: @SQ SN:NW_026963733.1 LN:30669 skipping SAM header line: @SQ SN:NW_026963734.1 LN:21233 skipping SAM header line: @SQ SN:NW_026963735.1 LN:20919 skipping SAM header line: @SQ SN:NW_026963736.1 LN:26026 skipping SAM header line: @SQ SN:NW_026963737.1 LN:15473 skipping SAM header line: @SQ SN:NW_026963738.1 LN:23824 skipping SAM header line: @SQ SN:NW_026963739.1 LN:19804 skipping SAM header line: @SQ SN:NW_026963740.1 LN:17713 skipping SAM header line: @SQ SN:NW_026963741.1 LN:20707 skipping SAM header line: @SQ SN:NW_026963742.1 LN:18963 skipping SAM header line: @SQ SN:NW_026963743.1 LN:21370 skipping SAM header line: @SQ SN:NW_026963744.1 LN:22821 skipping SAM header line: @SQ SN:NW_026963745.1 LN:20669 skipping SAM header line: @SQ SN:NW_026963746.1 LN:25286 skipping SAM header line: @SQ SN:NW_026963747.1 LN:21276 skipping SAM header line: @SQ SN:NW_026963748.1 LN:22489 skipping SAM header line: @SQ SN:NW_026963749.1 LN:18369 skipping SAM header line: @SQ SN:NW_026963750.1 LN:22802 skipping SAM header line: @SQ SN:NW_026963751.1 LN:24575 skipping SAM header line: @SQ SN:NW_026963752.1 LN:23655 skipping SAM header line: @SQ SN:NW_026963753.1 LN:26162 skipping SAM header line: @SQ SN:NW_026963754.1 LN:23060 skipping SAM header line: @SQ SN:NW_026963755.1 LN:23954 skipping SAM header line: @SQ SN:NW_026963756.1 LN:21792 skipping SAM header line: @SQ SN:NW_026963757.1 LN:32711 skipping SAM header line: @SQ SN:NW_026963758.1 LN:26150 skipping SAM header line: @SQ SN:NW_026963759.1 LN:24511 skipping SAM header line: @SQ SN:NW_026963760.1 LN:21863 skipping SAM header line: @SQ SN:NW_026963761.1 LN:29603 skipping SAM header line: @SQ SN:NW_026963762.1 LN:14940 skipping SAM header line: @SQ SN:NW_026963763.1 LN:20415 skipping SAM header line: @SQ SN:NW_026963764.1 LN:28644 skipping SAM header line: @SQ SN:NW_026963765.1 LN:26859 skipping SAM header line: @SQ SN:NW_026963766.1 LN:21572 skipping SAM header line: @SQ SN:NW_026963767.1 LN:11867 skipping SAM header line: @SQ SN:NW_026963768.1 LN:22422 skipping SAM header line: @SQ SN:NW_026963769.1 LN:19132 skipping SAM header line: @SQ SN:NW_026963770.1 LN:17338 skipping SAM header line: @SQ SN:NW_026963771.1 LN:24159 skipping SAM header line: @SQ SN:NW_026963772.1 LN:22295 skipping SAM header line: @SQ SN:NW_026963773.1 LN:15046 skipping SAM header line: @SQ SN:NW_026963774.1 LN:18598 skipping SAM header line: @SQ SN:NW_026963775.1 LN:22167 skipping SAM header line: @SQ SN:NW_026963776.1 LN:16973 skipping SAM header line: @SQ SN:NW_026963777.1 LN:18602 skipping SAM header line: @SQ SN:NW_026963778.1 LN:24241 skipping SAM header line: @SQ SN:NW_026963779.1 LN:27924 skipping SAM header line: @SQ SN:NW_026963780.1 LN:25424 skipping SAM header line: @SQ SN:NW_026963781.1 LN:28413 skipping SAM header line: @SQ SN:NW_026963782.1 LN:20838 skipping SAM header line: @SQ SN:NW_026963783.1 LN:22467 skipping SAM header line: @SQ SN:NW_026963784.1 LN:25012 skipping SAM header line: @SQ SN:NW_026963785.1 LN:13181 skipping SAM header line: @SQ SN:NW_026963786.1 LN:18105 skipping SAM header line: @SQ SN:NW_026963787.1 LN:18769 skipping SAM header line: @SQ SN:NW_026963788.1 LN:21775 skipping SAM header line: @SQ SN:NW_026963789.1 LN:26327 skipping SAM header line: @SQ SN:NW_026963790.1 LN:14514 skipping SAM header line: @SQ SN:NW_026963791.1 LN:20050 skipping SAM header line: @SQ SN:NW_026963792.1 LN:18784 skipping SAM header line: @SQ SN:NW_026963793.1 LN:20749 skipping SAM header line: @SQ SN:NW_026963794.1 LN:13251 skipping SAM header line: @SQ SN:NW_026963795.1 LN:20766 skipping SAM header line: @SQ SN:NW_026963796.1 LN:23492 skipping SAM header line: @SQ SN:NW_026963797.1 LN:20235 skipping SAM header line: @SQ SN:NW_026963798.1 LN:13457 skipping SAM header line: @SQ SN:NW_026963799.1 LN:17957 skipping SAM header line: @SQ SN:NW_026963800.1 LN:22384 skipping SAM header line: @SQ SN:NW_026963801.1 LN:31865 skipping SAM header line: @SQ SN:NW_026963802.1 LN:24022 skipping SAM header line: @SQ SN:NW_026963803.1 LN:26219 skipping SAM header line: @SQ SN:NW_026963804.1 LN:24043 skipping SAM header line: @SQ SN:NW_026963805.1 LN:28961 skipping SAM header line: @SQ SN:NW_026963806.1 LN:14045 skipping SAM header line: @SQ SN:NW_026963807.1 LN:15082 skipping SAM header line: @SQ SN:NW_026963808.1 LN:24314 skipping SAM header line: @SQ SN:NW_026963809.1 LN:20441 skipping SAM header line: @SQ SN:NW_026963810.1 LN:10923 skipping SAM header line: @SQ SN:NW_026963811.1 LN:26407 skipping SAM header line: @SQ SN:NW_026963812.1 LN:14166 skipping SAM header line: @SQ SN:NW_026963813.1 LN:10138 skipping SAM header line: @SQ SN:NW_026963814.1 LN:8703 skipping SAM header line: @SQ SN:NW_026963815.1 LN:16400 skipping SAM header line: @SQ SN:NC_007687.1 LN:18652 skipping SAM header line: @PG ID:Bismark VN:v0.24.2 CL:"bismark -genome ../01-bismark-init/ -p 8 -u 10000 -score_min L,0,-0.6 --non_directional -1 ../../data/raw-wgbs/105M_1.fastq.gz -2 ../../data/raw-wgbs/105M_2.fastq.gz -o ." skipping SAM header line: @PG ID:samtools PN:samtools PP:Bismark VN:1.20 CL:/srlab/programs/samtools-1.20/samtools view -bSh - skipping SAM header line: @PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:/srlab/programs/samtools-1.20/samtools view -h --threads 1 105M_1_bismark_bt2_pe.bam skipping SAM header line: @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:/srlab/programs/samtools-1.20/samtools view -bS --threads 1 - skipping SAM header line: @PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.20 CL:/srlab/programs/samtools-1.20/samtools view -h 105M_1_bismark_bt2_pe.deduplicated.bam Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '105M_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: No such file or directory at /srlab/programs/Bismark-0.24.2/bismark_methylation_extractor line 459, line 36.