Failure during chimera handling of ...

[antarikshtyagi]

Hi,

I am getting this error while running juicer pipeline on slurm at the mergesort step:

***! Failure during chimera handling of /gpfs/gibbs/pi/ycga/mane/at2253/wangSung/20221019_HiC/AS-FB_HiC//splits/AS-FB-HiC_AHV5HHDSX3_L001_001.fastq.gz

Based on previous error reports, I have updated gawk/awk but that did not fix the issue. Attached here is the debug folder: https://drive.google.com/drive/folders/1iwQfT4R7f10UtHK93L7cuYIXIqmj-60e?usp=sharing

Could you please help in fixing the issue?

Thanks Ant

[jlchen5]

I also update the gawk, but I still have the same problem!!!

[main] Real time: 2512.104 sec; CPU: 58695.419 sec
(-:  Align of /home/XXX/opt/juicer/splits/XXX_repl_1.fastq.gz.sam done successfully
sort: invalid option -- 't'
Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -o FILE    Write final output to FILE rather than standard output
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
  -@, --threads INT
             Set number of sorting and compression threads [1]
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
***! Failure during chimera handling of /home/XXX/opt/juicer/splits/XXX_repl_1.fastq.gz

[lychen83]

Hi there,

I met the same problem. Could you kindly let me how you resolved the problem? Best,

Lingyun

[jlchen5]

reinstall the gawk and make sure your awk is gawk

在 2022年12月28日，23:34，lychen83 @.***> 写道：



Hi there,

I met the same problem. Could you kindly let me how you resolved the problem? Best,

Lingyun

— Reply to this email directly, view it on GitHubhttps://github.com/aidenlab/juicer/issues/295#issuecomment-1366738309, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AOVZ54MA3MUSCUUOMFHWTQ3WPRMYDANCNFSM6AAAAAARTGQL3Y. You are receiving this because you commented.Message ID: @.***>

[pengzhen688]

I reinstalled gawk but it still didn't work，so I modified the juicer.sh and run awk separately, and it works. But I still don't know why it happens!!!

source ${juiceDir}/scripts/common/countligations.sh if [ -f "$name$ext.sam" ]; then echo "Skipping alignment as $name$ext.sam already exists" else bwa mem -SP5M $threadstring $refSeq $name1$ext $name2$ext > $name$ext.sam if [ $? -ne 0 ]; then echo "***! Alignment of $name1$ext $name2$ext failed." exit 1 else echo "(-: Align of $name$ext.sam done successfully" fi fi

and run touch male.fastq_abnorm.sam male.fastq_unmapped.sam
awk -v "fname1"=male.fastq_norm.txt -v "fname2"=male.fastq_abnorm.sam -v "fname3"=male.fastq_unmapped.sam -f /ds3200_1/users_root/pengzhen/software/juicer/CPU/common/chimeric_blacklist.awk male.fastq.sam It works successfully!!!