Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 255.

The full error message was:

Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN (zr3644_20)'

Caused by:
  Process `NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN (zr3644_20)` terminated with an error exit status (255)


Command executed:

  ln -sf $(readlink GCF_963853765.1_xbMagGiga1.1_genomic.fa) BismarkIndex/GCF_963853765.1_xbMagGiga1.1_genomic.fa
  
  bismark \
      -1 zr3644_20_R1_val_1_val_1_val_1.fq.gz -2 zr3644_20_R2_val_2_val_2_val_2.fq.gz \
      --genome BismarkIndex \
      --bam \
      --score_min L,0,-0.8 --non_directional --prefix zr3644_20 --multicore 2
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN":
      bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  chr NC_088853.1 (76070991 bp)
  chr NC_088854.1 (61469542 bp)
  chr NC_088855.1 (61039741 bp)
  chr NC_088856.1 (57946171 bp)
  chr NC_088857.1 (57274926 bp)
  chr NC_088858.1 (56905015 bp)
  chr NC_088859.1 (53672946 bp)
  chr NC_088860.1 (51133819 bp)
  chr NC_088861.1 (50364239 bp)
  chr NC_088862.1 (37310742 bp)
  chr NW_027062568.1 (15579 bp)
  chr NW_027062569.1 (16498 bp)
  chr NW_027062570.1 (4000 bp)
  chr NW_027062571.1 (36893 bp)
  chr NW_027062572.1 (51000 bp)
  chr NW_027062573.1 (2000 bp)
  chr NW_027062574.1 (37061 bp)
  chr NW_027062575.1 (49428 bp)
  chr NW_027062576.1 (49232 bp)
  chr NW_027062577.1 (17087 bp)
  chr NW_027062578.1 (34507 bp)
  chr NW_027062579.1 (64000 bp)
  chr NW_027062580.1 (24229 bp)
  chr NW_027062581.1 (5000 bp)
  chr NW_027062582.1 (18808 bp)
  chr NW_027062583.1 (1000 bp)
  chr NW_027062584.1 (74000 bp)
  chr NW_027062585.1 (39334 bp)
  chr NW_027062586.1 (258015 bp)

Command error:
  
  Input files are zr3644_20.zr3644_20_R1_val_1_val_1_val_1.fq.gz.temp.2_C_to_T.fastq and zr3644_20.zr3644_20_R1_val_1_val_1_val_1.fq.gz.temp.2_G_to_A.fastq and zr3644_20.zr3644_20_R2_val_2_val_2_val_2.fq.gz.temp.2_C_to_T.fastq and zr3644_20.zr3644_20_R2_val_2_val_2_val_2.fq.gz.temp.2_G_to_A.fastq (FastQ)
  Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/strigg/analyses/20250401_methylseq/work/9d/e051ee675531cecf8e8dc3712d55e2/BismarkIndex/ with the specified options: -q --score-min L,0,-0.8 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
  
  Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_20.zr3644_20_R1_val_1_val_1_val_1.fq.gz.temp.2_C_to_T.fastq and zr3644_20.zr3644_20_R2_val_2_val_2_val_2.fq.gz.temp.2_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
  Found first alignment:
  A00742:173:HMGVGDSXY:2:1101:4435:1000_1:N:0:NCGTTGGT+GGAAGTAT/1	77	*	0	0	*	*	0	0	TAAAATTATTAATTATAATAAAAATAATTTTTAAATATTTATTTTTTTATAAAATATAATATATAATTTTTAAATATTTAAAAATATTTATATATAATTATATTATTAAATATAT	FFFFFF:F:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:	YT:Z:UP
  A00742:173:HMGVGDSXY:2:1101:4435:1000_2:N:0:NCGTTGGT+GGAAGTAT/2	141	*	0	0	*	*	0	0	ATTTTATTAAAATATAAAATTTATTTTTAAAAAAAATAAATAATATATATTTAATAATATAATTATATATAAATATTTTTAAATATTTAAAAATTATATATTATATTTTATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
  Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_20.zr3644_20_R1_val_1_val_1_val_1.fq.gz.temp.2_G_to_A.fastq and zr3644_20.zr3644_20_R2_val_2_val_2_val_2.fq.gz.temp.2_C_to_T.fastq, with the options: -q --score-min L,0,-0.8 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
  Found first alignment:
  A00742:173:HMGVGDSXY:2:1101:4435:1000_1:N:0:NCGTTGGT+GGAAGTAT/1	77	*	0	0	*	*	0	0	TAAAATCATTAACTACAACAAAAATAATTTTTAAATACTTATCTTCCTATAAAATACAATATACAACCTTCAAATATTTAAAAATATTTATATACAACTATATTATCAAACACAT	FFFFFF:F:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:	YT:Z:UP
  A00742:173:HMGVGDSXY:2:1101:4435:1000_2:N:0:NCGTTGGT+GGAAGTAT/2	141	*	0	0	*	*	0	0	ATTTTATTAGAATGTGAAATTTATTTTTAAAAAGAATGAGTAATATGTGTTTGATAATATAGTTGTATATAAATATTTTTAAATATTTGAAGGTTGTATATTGTATTTTATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
  Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_20.zr3644_20_R1_val_1_val_1_val_1.fq.gz.temp.2_G_to_A.fastq and zr3644_20.zr3644_20_R2_val_2_val_2_val_2.fq.gz.temp.2_C_to_T.fastq, with the options: -q --score-min L,0,-0.8 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
  Found first alignment:
  A00742:173:HMGVGDSXY:2:1101:4435:1000_1:N:0:NCGTTGGT+GGAAGTAT/1	77	*	0	0	*	*	0	0	TAAAATCATTAACTACAACAAAAATAATTTTTAAATACTTATCTTCCTATAAAATACAATATACAACCTTCAAATATTTAAAAATATTTATATACAACTATATTATCAAACACAT	FFFFFF:F:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:	YT:Z:UP
  A00742:173:HMGVGDSXY:2:1101:4435:1000_2:N:0:NCGTTGGT+GGAAGTAT/2	141	*	0	0	*	*	0	0	ATTTTATTAGAATGTGAAATTTATTTTTAAAAAGAATGAGTAATATGTGTTTGATAATATAGTTGTATATAAATATTTTTAAATATTTGAAGGTTGTATATTGTATTTTATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
  Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_20.zr3644_20_R1_val_1_val_1_val_1.fq.gz.temp.2_C_to_T.fastq and zr3644_20.zr3644_20_R2_val_2_val_2_val_2.fq.gz.temp.2_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
  Found first alignment:
  A00742:173:HMGVGDSXY:2:1101:4435:1000_1:N:0:NCGTTGGT+GGAAGTAT/1	77	*	0	0	*	*	0	0	TAAAATTATTAATTATAATAAAAATAATTTTTAAATATTTATTTTTTTATAAAATATAATATATAATTTTTAAATATTTAAAAATATTTATATATAATTATATTATTAAATATAT	FFFFFF:F:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:	YT:Z:UP
  A00742:173:HMGVGDSXY:2:1101:4435:1000_2:N:0:NCGTTGGT+GGAAGTAT/2	141	*	0	0	*	*	0	0	ATTTTATTAAAATATAAAATTTATTTTTAAAAAAAATAAATAATATATATTTAATAATATAATTATATATAAATATTTTTAAATATTTAAAAATTATATATTATATTTTATA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	YT:Z:UP
  
  >>> Writing bisulfite mapping results to zr3644_20.zr3644_20_R1_val_1_val_1_val_1.fq.gz.temp.2_bismark_bt2_pe.bam <<<
  
  
  Reading in the sequence files zr3644_20_R1_val_1_val_1_val_1.fq.gz.temp.2 and zr3644_20_R2_val_2_val_2_val_2.fq.gz.temp.2
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1116:14398:32534_1:N:0:GCGTTGGT+GGAAGTAT	NW_027062570.1	1
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1130:26793:28040_1:N:0:GCGTTGGT+GGAAGTAT	NW_027062573.1	1898
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1131:28275:28197_1:N:0:GCGTTGGT+GGAAGTAT	NW_027062573.1	1899
  Processed 1000000 sequence pairs so far
  Processed 1000000 sequence pairs so far
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1138:31331:6151_1:N:0:GCGTTGGT+GGAAGTAT	NW_027062570.1	1
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1141:20735:4335_1:N:0:GCGTTGGT+GGAAGTAT	NW_027062570.1	3908
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1141:20292:28244_1:N:0:GCGTTGGT+GGAAGTAT	NW_027062570.1	3909
  Processed 2000000 sequence pairs so far
  Processed 2000000 sequence pairs so far
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1203:23529:15060_1:N:0:GCGTTGGT+GGAAGTAT	NW_027062570.1	1
  Processed 3000000 sequence pairs so far
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1227:5647:27117_1:N:0:GCGTTGGT+GGAAGTAT	NW_027062570.1	1
  Processed 3000000 sequence pairs so far
  Processed 4000000 sequence pairs so far
  Processed 5000000 sequence pairs so far
  Processed 6000000 sequence pairs so far
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1353:6334:24048_1:N:0:GCGTTGGT+GGAAGTAT	NW_027062570.1	3895
  Processed 7000000 sequence pairs so far
  (ERR): bowtie2-align died with signal 9 (KILL) 
  Use of uninitialized value $flag_2 in numeric eq (==) at /usr/local/bin/bismark line 3289, <__ANONIO__> line 14477443.
  Chromosome number extraction failed for *
  (ERR): bowtie2-align died with signal 13 (PIPE) 
  (ERR): bowtie2-align died with signal 13 (PIPE) 
  (ERR): bowtie2-align died with signal 13 (PIPE) 

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20250401_methylseq/work/fa/e40a6be181600a7c1f9acd93de2c77

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-bismark-0.24.2--hdfd78af_0.img

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`