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I am running an nf-core/hic pipeline for breast samples (Total 6 samples including replicates) 500 Million reads each.
I am getting the following error
executor > local (4)
[1f/560b97] process > get_software_versions [100%] 1 of 1, cached: 1 ✔
[e6/dd369f] process > makeChromSize (genome.fa) [100%] 1 of 1, cached: 1 ✔
[3e/5eccce] process > getRestrictionFragments (genome.fa [^GATC]) [100%] 1 of 1, cached: 1 ✔
[5c/13bee9] process > bowtie2_end_to_end (HiChIP_MCF10A-B_S8_R2_001.35) [100%] 234 of 234, cache...
[20/529041] process > trim_reads (HiChIP_MCF10A-B_S8_R2_001.35) [100%] 234 of 234, cache...
[c0/19592a] process > bowtie2_on_trimmed_reads (HiChIP_MCF10A-B_S8_R2_001.27) [100%] 234 of 234, cache...
[37/3b2c66] process > merge_mapping_steps (HiChIP_MCF10A-B_S8_001.34 = HiChIP_MC... [100%] 234 of 234, cache...
[63/d5a7a2] process > combine_mapped_files (HiChIP_MCF10A-B_S8_001.26 = HiChIP_M... [100%] 117 of 117, cache...
[5e/368d6e] process > get_valid_interaction (HiChIP_MCF10A-B_S8_001) [100%] 117 of 117, cache...
[84/34a0f2] process > remove_duplicates (HiChIP_MCF10A-A_S7_001) [100%] 3 of 3, failed: 3...
[a9/485599] process > merge_sample (mRSstat) [100%] 8 of 8, cached: 8 ✔
[- ] process > build_contact_maps -
[- ] process > run_ice -
[- ] process > generate_cool -
[- ] process > multiqc -
[b7/f6bd1d] process > output_documentation (1) [100%] 1 of 1, cached: 1 ✔
Error executing process > 'remove_duplicates (HiChIP_MCF10A-B_S8_001)'
Caused by:
Process `remove_duplicates (HiChIP_MCF10A-B_S8_001)` terminated with an error exit status (137)
Command exit status:
137
Command output:
(empty)
Command error:
.command.sh: line 5: 31 Killed sort -T /tmp/ -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m HiChIP_MCF10A-B_S8_001.3_bwt2pairs.validPairs HiChIP_MCF10A-B_S8_001.21_bwt2pairs.validPairs
32 Done | awk -F"\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=$2 || c2!=$5 || s1!=$3 || s2!=$6){print;c1=$2;c2=$5;s1=$3;s2=$6}' > HiChIP_MCF10A-B_S8_001.allValidPairs
Work dir:
/mnt/hichip_fastq/work/fe/551ceae621f99884fd3f0b8c061957
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`
Hi,
This is a memory issue.
You should increase the resource for this job.
By default, it is running with 12GB of RAM which seems to not be enough in your case.
I would suggest to create your own config file and to change the RAM for this process ;
process {
withName:remove_duplicates {
memory = 40.Gb
}
}
Hello,
I am running an nf-core/hic pipeline for breast samples (Total 6 samples including replicates) 500 Million reads each.
I am getting the following error
The following is the script I ran
I tried to run with version 1.3.0 but the pipeline couldn't able to complete the bowtie2 end-to-end process so I am running with version 1.0.0.
Any thoughts?
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