Open antarikshtyagi opened 1 year ago
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
Hi there,
I met the same problem. Could you kindly let me how you resolved the problem? Best,
Lingyun
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: @.***>
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!!!
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