tag2collapse.pl was killed

[yang chen]

Hi,

    When I run the code, it finally was killed. In my virtual machine, it has 10 cores and 88 GB memory. 

    The size of "$px".UMI.tag.norRNA.bed is 5 GB. But the  "$px".UMI.tag.uniq.bed is only 44 MB after the code was killed. Could you give me some suggestions about the parameters adjustment to make it run? Thanks. 

 

1337: TTTTGAGACA [1], relative abundance=1.000 reliability=159.546

1338: TTTTGCATAC [1], relative abundance=1.000 reliability=159.546

1339: TTTTTGCAGG [1], relative abundance=1.000 reliability=159.546

1340: TTTTTTAGAT [1], relative abundance=1.000 reliability=159.546

s4_PCR.sh: line 68: 31251 Killed                  perl /usr/local/CTK/tag2collapse.pl -big -v --random-barcode -EM 30 --seq-error-model alignment -weight --weight-in-name --keep-max-score --keep-tag-name "$px".UMI.tag.norRNA.bed "$px".UMI.tag.uniq.bed

 

Best regards,

Yang Chen 

[Chaolin Zhang]

Hi Yang,

If you share your input file, we can help to take a look.

Chaolin

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[yang chen]

Hi Chaolin,

     The format of input file is as follows. I used STAR to do mapping. 

tail -10   f1/GFP-IN/GFP-IN_ATTCAGAA_L006_R1.SE.trim2.UMI.tag.norRNA.bed

chrY 59326464 59326513 HISEQ:341:CCW0RANXX:6:2309:18748:89872#1#ACACGAGCAG 0 - 59326464 59326513 0 1 490

chrY 59329250 59329289 HISEQ:341:CCW0RANXX:6:2310:12324:43265#1#CTACTTACTA 1 - 59329250 59329289 0 1 390

chrY 59329523 59329589 HISEQ:341:CCW0RANXX:6:2111:4530:86685#1#CCCACCACAG 3 - 59329523 59329589 0 1 660

chrY 59343244 59343295 HISEQ:341:CCW0RANXX:6:1203:3480:22746#1#ACCCAGCCCG 0 - 59343244 59343295 0 1 510

chrY 59343425 59343466 HISEQ:341:CCW0RANXX:6:2206:14709:62271#1#CATACCCTTG 0 - 59343425 59343466 0 1 410

chrY 59344354 59344401 HISEQ:341:CCW0RANXX:6:1103:2115:94171#1#TCCTTGTGCT 0 - 59344354 59344401 0 1 470

chrY 59345758 59345820 HISEQ:341:CCW0RANXX:6:2215:4991:87963#1#AACCTTTACC 0 - 59345758 59345820 0 1 620

chrY 59347753 59347794 HISEQ:341:CCW0RANXX:6:2103:2558:51275#1#ATATGGCAGT 0 - 59347753 59347794 0 1 410

chrY 59349350 59349416 HISEQ:341:CCW0RANXX:6:2103:1401:62758#1#CCCCAAATAC 1 - 59349350 59349416 0 1 660

chrY 59349388 59349454 HISEQ:341:CCW0RANXX:6:2312:6073:43690#1#CTCCGCCGAC 0 - 59349388 59349454 0 1 660

Thanks very much.

Best regards,

Yang Chen 

[Huijuan Feng]

Hi Yang,

The input file you provided seems to have around 60% reads mapped to GL000220.1 contig (rRNA mostly). The program failed when trying to collapse 38,834,778 tags on this contig, probably ran out of memory. By removing rRNA reads should be able to solve your problem.

Best,

Huijuan

[yang chen]

Hi Huijuan,

     Thanks very much. I will remove the GL** contig and run them again. 

Best regards,

Yang Chen 

[Huijuan Feng]

You're welcome. Pls let me know if you have any questions after rerun. 

Best,

Huijuan