Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/geoduck/v074/ (absolute path is '/gscratch/srlab/sr320/data/geoduck/v074/)' FastQ format assumed (by default) Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/0821-ba'): /gscratch/scrubbed/sr320/0821/Pg_val_1.fq.gz /gscratch/scrubbed/sr320/0821/Pg_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/0821-ba Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/sr320/0821/Pg_val_1.fq.gz and /gscratch/scrubbed/sr320/0821/Pg_val_2.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file Pg_val_1.fq.gz to Pg_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file Pg_val_1.fq.gz (1237279577 sequences in total) Writing a G -> A converted version of the input file Pg_val_2.fq.gz to Pg_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file Pg_val_2.fq.gz (1237279577 sequences in total) Input files are Pg_val_1.fq.gz_C_to_T.fastq and Pg_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from Pg_val_1.fq.gz_C_to_T.fastq and Pg_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1512:1956_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 NGTTTATATGTATGTATTATATTTGTGTAGGTATTGTATTTGATAAGGAT #<<>> Writing bisulfite mapping results to Pg_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/sr320/0821/Pg_val_1.fq.gz and /gscratch/scrubbed/sr320/0821/Pg_val_2.fq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2303:16672:27349_1:N:0:ATCACG PGA_scaffold9__45_contigs__length_38581958 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far slurmstepd: error: *** JOB 1207496 ON n2441 CANCELLED AT 2019-08-21T16:14:50 DUE TO NODE FAILURE, SEE SLURMCTLD LOG FOR DETAILS ***