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_6)'

Caused by:
  Process `NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN (zr3644_6)` 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_6_R1_val_1_val_1_val_1.fq.gz -2 zr3644_6_R2_val_2_val_2_val_2.fq.gz \
      --genome BismarkIndex \
      --bam \
      --score_min L,0,-0.8 --non_directional --prefix zr3644_6 --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:
  Found first alignment:
  A00742:173:HMGVGDSXY:2:1101:4128:1000_1:N:0:NATTAGTG+TATGTAGT/1	99	NC_088859.1_CT_converted	11770649	40	40M1D75M	=	11770657	121	ATTTATTTAATATGTATAGAAATGTATATTTTATTGTGGTAAAAAAAATTTTATTATATATGTAAATGTATTTGTGGATAATTTGAAATGAATTAGTGTGTTGGAAGTTATTTGT	FFFFFFFFFFFFFFF:F:FF,,:FFFF,F:::,,FF,FFF:,F:FFFFF,,F,F,FF:FFFFF,:F:F,,,,,F:FF,F,:FFFFF,:,FF,,,,F,F,,:FFF,,FF,,,F,F:	AS:i:-20	XN:i:0	XM:i:2	XO:i:1	XG:i:1	NM:i:3	MD:Z:40^A14A44T15	YS:i:-26	YT:Z:CP
  A00742:173:HMGVGDSXY:2:1101:4128:1000_2:N:0:NATTAGTG+TATGTAGT/2	147	NC_088859.1_CT_converted	11770657	40	32M1D80M	=	11770649	-121	AAGATGTATAGAAATGTATATTTGATTGTGGTAAAAAAAATTTTATAATATATGTAAATGTATGTGTGGATAATTTGAAATGAATTAGTGTTTTGGAAGTTATTTGTAATGG	FF,F,F,:,,F,:,,FF,,:,:F,:,:F,FF,F,:FF,F:::::F,F:,,,:,F:,F,,F:F:,,F:FFF,F,F,:FFFF,F:,,,FFFFFF,:FF,,F,:::,,FFFF:FF	AS:i:-26	XN:i:0	XM:i:3	XO:i:1	XG:i:1	NM:i:4	MD:Z:2T20T8^A31T48	YS:i:-20	YT:Z:CP
  Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_6.zr3644_6_R1_val_1_val_1_val_1.fq.gz.temp.2_G_to_A.fastq and zr3644_6.zr3644_6_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:2:1101:1832:1000_1:N:0:NATTAGTG+TATGTAGT/1	83	NC_088856.1_CT_converted	13082717	2	20M2D15M1D70M1D4M1I5M	=	13082695	-140	AAGGGTGATTTGGGAGTTATATTGTTTTTTATAGTAAAAAATTGTAATTTATGGTGTTAGTTTTGGATTGATTAATTTTATTTTTAAATATATTTTGTATAAATATTTGATTTTA	FFF,F:FF,,::::FFF:FF,FFF:F,,F:F:F:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:-89	XS:i:-77	XN:i:0	XM:i:9	XO:i:4	XG:i:5	NM:i:14	MD:Z:1T2A15^AG9G5^A51T3A6G0G0A5^G5A3	YS:i:-74	YT:Z:CP
  A00742:173:HMGVGDSXY:2:1101:1832:1000_2:N:0:NATTAGTG+TATGTAGT/2	163	NC_088856.1_CT_converted	13082695	2	18M1I1M2I23M2D15M1D54M	=	13082717	140	TGGTTTTTGGTTTGAAAATATTTGGAAGGGTGATTTGGGAGTTATATTGTTTTTTATAGTAAAAAATTGTAATTTATGGTGTTAGTTTTGGATTGATTAATTTTATTTTTAAAT	FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF	AS:i:-74	XS:i:-89	XN:i:0	XM:i:6	XO:i:4	XG:i:6	NM:i:12	MD:Z:0A0A21T2A15^AG9G5^A51T2	YS:i:-89	YT:Z:CP
  Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_6.zr3644_6_R1_val_1_val_1_val_1.fq.gz.temp.1_C_to_T.fastq and zr3644_6.zr3644_6_R2_val_2_val_2_val_2.fq.gz.temp.1_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:2:1101:4128:1000_1:N:0:NATTAGTG+TATGTAGT/1	77	*	0	0	*	*	0	0	ATTTATTTAATATATATAAAAATATATATTTTATTATAATAAAAAAAATTTTATCATATATATAAATATATTTATAAATAATTTAAAATAAATTAATATATTAAAAATTATTTAT	FFFFFFFFFFFFFFF:F:FF,,:FFFF,F:::,,FF,FFF:,F:FFFFF,,F,F,FF:FFFFF,:F:F,,,,,F:FF,F,:FFFFF,:,FF,,,,F,F,,:FFF,,FF,,,F,F:	YT:Z:UP
  A00742:173:HMGVGDSXY:2:1101:4128:1000_2:N:0:NATTAGTG+TATGTAGT/2	141	*	0	0	*	*	0	0	TTATTATAAATAATTTTTAAAATATTAATTTATTTTAAATTATTTATATATATATTTATATATATTATAAAATTTTTTTTATTATAATTAAATATATATTTTTATATATTTT	FF:FFFF,,:::,F,,FF:,FFFFFF,,,:F,FFFF:,F,F,FFF:F,,:F:F,,F,:F,:,,,:F,F:::::F,FF:,F,FF,F:,:,F:,:,,FF,,:,F,,:,F,F,FF	YT:Z:UP
  Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_6.zr3644_6_R1_val_1_val_1_val_1.fq.gz.temp.2_G_to_A.fastq and zr3644_6.zr3644_6_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:2:1101:1832:1000_1:N:0:NATTAGTG+TATGTAGT/1	77	*	0	0	*	*	0	0	TAAAATTAAATATTTATATAAAATATATTTAAAAATAAAATTAATTAATTTAAAATTAATATTATAAATTATAATTTTTTATTATAAAAAATAATATAATTTTTAAATTATTTTT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:F:F:F,,F:FFF,FF:FFF::::,,FF:F,FFF	YT:Z:UP
  A00742:173:HMGVGDSXY:2:1101:1832:1000_2:N:0:NATTAGTG+TATGTAGT/2	141	*	0	0	*	*	0	0	TAATTTTTAATTTAAAAATATTTAAAAAAATAATTTAAAAATTATATTATTTTTTATAATAAAAAATTATAATTTATAATATTAATTTTAAATTAATTAATTTTATTTTTAAAT	FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF	YT:Z:UP
  
  >>> Writing bisulfite mapping results to zr3644_6.zr3644_6_R1_val_1_val_1_val_1.fq.gz.temp.1_bismark_bt2_pe.bam <<<
  
  Found first alignment:
  A00742:173:HMGVGDSXY:2:1101:4128:1000_1:N:0:NATTAGTG+TATGTAGT/1	77	*	0	0	*	*	0	0	ATTTATTTAATATATATAAAAATATATATTTTATTATAATAAAAAAAATTTTATCATATATATAAATATATTTATAAATAATTTAAAATAAATTAATATATTAAAAATTATTTAT	FFFFFFFFFFFFFFF:F:FF,,:FFFF,F:::,,FF,FFF:,F:FFFFF,,F,F,FF:FFFFF,:F:F,,,,,F:FF,F,:FFFFF,:,FF,,,,F,F,,:FFF,,FF,,,F,F:	YT:Z:UP
  A00742:173:HMGVGDSXY:2:1101:4128:1000_2:N:0:NATTAGTG+TATGTAGT/2	141	*	0	0	*	*	0	0	TTATTATAAATAATTTTTAAAATATTAATTTATTTTAAATTATTTATATATATATTTATATATATTATAAAATTTTTTTTATTATAATTAAATATATATTTTTATATATTTT	FF:FFFF,,:::,F,,FF:,FFFFFF,,,:F,FFFF:,F,F,FFF:F,,:F:F,,F,:F,:,,,:F,F:::::F,FF:,F,FF,F:,:,F:,:,,FF,,:,F,,:,F,F,FF	YT:Z:UP
  Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_6.zr3644_6_R1_val_1_val_1_val_1.fq.gz.temp.2_C_to_T.fastq and zr3644_6.zr3644_6_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))
  
  Reading in the sequence files zr3644_6_R1_val_1_val_1_val_1.fq.gz.temp.1 and zr3644_6_R2_val_2_val_2_val_2.fq.gz.temp.1
  Found first alignment:
  A00742:173:HMGVGDSXY:2:1101:4128:1000_1:N:0:NATTAGTG+TATGTAGT/1	77	*	0	0	*	*	0	0	ATTTATTTAATATGTATAGAAATGTATATTTTATTGTGGTAAAAAAAATTTTATTATATATGTAAATGTATTTGTGGATAATTTGAAATGAATTAGTGTGTTGGAAGTTATTTGT	FFFFFFFFFFFFFFF:F:FF,,:FFFF,F:::,,FF,FFF:,F:FFFFF,,F,F,FF:FFFFF,:F:F,,,,,F:FF,F,:FFFFF,:,FF,,,,F,F,,:FFF,,FF,,,F,F:	YT:Z:UP
  A00742:173:HMGVGDSXY:2:1101:4128:1000_2:N:0:NATTAGTG+TATGTAGT/2	141	*	0	0	*	*	0	0	CCATTACAAATAACTTCCAAAACACTAATTCATTTCAAATTATCCACACATACATTTACATATATTATAAAATTTTTTTTACCACAATCAAATATACATTTCTATACATCTT	FF:FFFF,,:::,F,,FF:,FFFFFF,,,:F,FFFF:,F,F,FFF:F,,:F:F,,F,:F,:,,,:F,F:::::F,FF:,F,FF,F:,:,F:,:,,FF,,:,F,,:,F,F,FF	YT:Z:UP
  
  >>> Writing bisulfite mapping results to zr3644_6.zr3644_6_R1_val_1_val_1_val_1.fq.gz.temp.2_bismark_bt2_pe.bam <<<
  
  
  Reading in the sequence files zr3644_6_R1_val_1_val_1_val_1.fq.gz.temp.2 and zr3644_6_R2_val_2_val_2_val_2.fq.gz.temp.2
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1101:29767:30311_1:N:0:CATTAGTG+TATGTAGT	NW_027062570.1	3928
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1131:9173:2785_1:N:0:CATTAGTG+TATGTAGT	NW_027062570.1	1
  Processed 1000000 sequence pairs so far
  Processed 1000000 sequence pairs so far
  Processed 2000000 sequence pairs so far
  Processed 3000000 sequence pairs so far
  Processed 2000000 sequence pairs so far
  Chromosomal sequence could not be extracted for	A00742:173:HMGVGDSXY:2:1237:21477:23187_1:N:0:CATTAGTG+TATGTAGT	NW_027062570.1	3918
  Processed 3000000 sequence pairs so far
  (ERR): bowtie2-align died with signal 9 (KILL) 
  (ERR): bowtie2-align died with signal 9 (KILL) 
  Use of uninitialized value $alignment_score_2 in concatenation (.) or string at /usr/local/bin/bismark line 3378,  line 12676024.
  Use of uninitialized value $MD_tag_2 in concatenation (.) or string at /usr/local/bin/bismark line 3378,  line 12676024.
  Failed to extract alignment score 2 () and MD tag ()!
  last alignment 1: A00742:173:HMGVGDSXY:2:1234:18611:21856_1:N:0:CATTAGTG+TATGTAGT/1	99	NC_088854.1_CT_converted	32160553	18	115M	=	32160648	209	ATTAATAATATTATTTTATTGGTTAAGGATTTAAGGTTATTTTTGGTTTTTTAATGGATATTTTATTTAAGAGGATTTTTTGTATTTTTATAGTGGTTGAATTATGTTGAAGTTT	FF:FFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFF:FF:FFFFFFFF:FFFF::FFFFFF:FFF:FFFFFF:FFFFFFFFFFFFFFFFFF	AS:i:-6	XS:i:-26	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:83T31	YS:i:-6	YT:Z:CP
  last alignment 2: A00742:173:HMGVGDSXY:2:1234:18611:21856_2:N:0:CATTAGTG+TATGTAGT/2	147	NC_088854.1_CT_converted	32160648	18	114M	=	32160553	-209	GTTGAATTATGTTGAAGTTTTTTATTTTGTAAAATGATATAAGATGAATTTTGATTTTTTTATAGGTGAATAATAATTTTATATGATTGATTTAATATTAAAGGTGATTTTTAG	FFFFF:FFFFFFFF,FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF
  (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/39/114b73bfc07d4bb5a7efa62b9e82f6

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

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`