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GATB / gatb-minia-pipeline

GATB Minia assembly pipeline
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Execution of 'perl tools/sga-deinterleave.pl' #16

Closed Shirley-Q closed 4 years ago

Shirley-Q commented 5 years ago

Hi, There was an error as fllowed. I can not find the reason. could you help me? (2019-05-25 03:32:29) Execution of 'perl tools/sga-deinterleave.pl'. Command line: perl /home/emma/gatb-minia-pipeline/tools/sga-deinterleave.pl trim.fq assembly.lib0_1.fq assembly.lib0_2.fq Found two consecutive /1 read headers, exiting; (last header: @RM2|S1|R22652116/1) at /home/emma/gatb-minia-pipeline/tools/sga-deinterleave.pl line 52, line 8. (2019-05-25 03:32:30) Execution of 'perl tools/sga-deinterleave.pl' failed. Command line: perl /home/emma/gatb-minia-pipeline/tools/sga-deinterleave.pl trim.fq assembly.lib0_1.fq assembly.lib0_2.fq

Best wishes, Shirley

Shirley-Q commented 5 years ago

(2019-05-25 03:47:59) Execution of 'python BESST/runBESST'. Command line: /home/emma/gatb-minia-pipeline/tools/memused python /home/emma/gatb-minia-pipeline/BESST/runBESST -c assembly_k31.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000 Number of initial contigs: 32 There was another error. Estimating insert size from 48 mappings with quality over --min_mapq 11. To few valid read alignments exists to compute mean and variance of library (need at least 1000 observations). Got only 47 valid alignments. Please specify -m and -s to the program. Printing out scaffolds produced in earlier steps... terminating... maximal memory used: 85 MB Error: BESST returned no results in assembly_besst/

rchikhi commented 5 years ago

Hi Shirley, sorry for the late response. Did you end up figuring the issue? There might be a problem with the input dataset.

Shirley-Q commented 5 years ago

yes， I re-install the atb-minia-pipeline. And No longer have this problem. But I have new error as described in nohup.out file. Thank you very much!

best wishes, Shirley

------------------ 原始邮件 ------------------ 发件人: "Rayan Chikhi"notifications@github.com; 发送时间: 2019年6月2日(星期天) 晚上8:50 收件人: "GATB/gatb-minia-pipeline"gatb-minia-pipeline@noreply.github.com; 抄送: "乔雪姣"1678141559@qq.com;"State change"state_change@noreply.github.com; 主题: Re: [GATB/gatb-minia-pipeline] Execution of 'perltools/sga-deinterleave.pl' (#16)

Hi Shirley, sorry for the late response. Did you end up figuring the issue?

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rchikhi commented 5 years ago

What's the contents of this nohup.out file?