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CIRICount

Issue #128 new
guojiaqi created an issue

hi, i am using the circrna-seq pipeline to analyze data, every thing is fine until it runs to the step of Readcount Analysis. it appears: CIRICount ERROR :: system args failed: 35072 (mkdir -p /media/yu/NGSDATA/circRNA/results//circRNAs_results/ ;CIRI_v1.2.pl -P -I /media/yu/NGSDATA/circRNA/results//bwa_results/SRR3475954_bwa.sam -O /media/yu/NGSDATA/circRNA/results//circRNAs_results/SRR3475954_bwa.ciri -A /media/yu/NGSDATA/circRNA/GRCh38/GRCh38.gtf -F /media/yu/NGSDATA/circRNA/GRCh38/GRCh38.fa -G /media/yu/NGSDATA/circRNA/results//miARma_logfile.30558.log > /media/yu/NGSDATA/circRNA/results//miARma_logfile.30558.log 2>&1) at lib/CbBio/RNASeq/Readcount.pm line 595, <RESULTS> line 78..

i hope you can help me with this , thanks

Comments (16)

  5. guojiaqi reporter

    i have six samples to analyze. and before the problem occur, the other 2 samples seem to run correctly and produced the *bwa.ciri file. SRR3475952.sam and SRR3475953 are about 12.5G and 22.9G, and SRR3475954 is about 35.7G. I don' know if it is involved with the problem.

  6. Eduardo Andres Leon

    According with the log file, the process was killed. Do you have enough free RAM ? For a 36G file ... you will need a lot of RAM memory

  8. Eduardo Andres Leon

    My guess: 16GB RAM for a 36GB file is not enough. Could you try to perform the whole analysis with samples smaller than 23GB ?

  9. guojiaqi reporter

    how many RAM do you think it will need according with 36G files and are there any other solution do you suggest

  11. Eduardo Andres Leon

    I'm not sure about the RAM, I know that BWA and CIRI needs a lot, the other software are not so demanding. I'm using a 128GB RAM machine and I've processed files up to 44GB

    Have you try to use fewer processors/cores (1 or 2) ?

  12. guojiaqi reporter

    i have not try to use fewer processors/cores. when i performed the analysis, i just perform the ini file and i dont kown how to set it

  15. guojiaqi reporter

    hi, the document of circRNA-seq says that the alignment of bwa outputs bam files, but it produced sam files in my run. i think if it outputs bam files,then the file will become smaller. but i don't know how to set .could you help me?

  16. Eduardo Andres Leon

    Yes, BWA in miARma produced bam files (using samtools in between), but we changed this behaviour some releases ago. Now with the new version (1.8), that will be published this year, the documentation will be updated and in the case of circRNAs, 3 softwares will be added

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