我正在尝试建立一条蛇形管道,并且它抱怨缺少MissingOutputException:
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cluster nodes: 8
Job counts:
count jobs
1 add_replace_readgroups
1 all
1 annotate_nirvana
1 apply_bqsr
1 base_recalibrator
1 bwa_aln1
1 bwa_aln2
1 bwa_sampe
1 flagstats
1 haplotypecaller
1 intervals
1 isize
1 json2vcf
1 mark_dups
1 mod_sam
1 region_coverage
1 sam2bam
17
[Wed Jul 17 09:03:04 2019]
rule bwa_aln2:
input: C052007W-B.2.fq.gz, /mnt/storage/projects/hiv_data/refs/PKD_GANAB/PKD.fasta
output: tmp/C052007W-B.2.sai
log: logs/bwa_aln2/C052007W-B.log
jobid: 8
wildcards: sample=C052007W-B
threads: 8
bwa aln -t 8 -q 15 -e 50 -f tmp/C052007W-B.2.sai /mnt/storage/projects/hiv_data/refs/PKD_GANAB/PKD.fasta C052007W-B.2.fq.gz 2> logs/bwa_aln2/C052007W-B.log
Submitted job 8 with external jobid 'Submitted batch job 283790'.
[Wed Jul 17 09:03:04 2019]
rule bwa_aln1:
input: C052007W-B.1.fq.gz, /mnt/storage/projects/hiv_data/refs/PKD_GANAB/PKD.fasta
output: tmp/C052007W-B.1.sai
log: logs/bwa_aln1/C052007W-B.log
jobid: 7
wildcards: sample=C052007W-B
threads: 8
bwa aln -t 8 -q 15 -e 50 -f tmp/C052007W-B.1.sai /mnt/storage/projects/hiv_data/refs/PKD_GANAB/PKD.fasta C052007W-B.1.fq.gz 2> logs/bwa_aln1/C052007W-B.log
Submitted job 7 with external jobid 'Submitted batch job 283791'.
Waiting at most 30 seconds for missing files.
MissingOutputException in line 63 of /mnt/storage/home/kimy/projects/automate_CP/scripts/Snakefile:
Missing files after 30 seconds:
tmp/C052007W-B.2.sai
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Waiting at most 30 seconds for missing files.
[Wed Jul 17 09:04:04 2019]
Finished job 7.
1 of 17 steps (6%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /mnt/storage/home/kimy/projects/automate_CP/CP0340/.snakemake/log/2019-07-17T090304.049684.snakemake.log
我正在使用以下命令行运行它:
/mnt/storage/home/kimy/software/miniconda3/bin/snakemake \
-s /mnt/storage/home/kimy/projects/automate_CP/scripts/Snakefile \
-j 8 \
-p \
--latency-wait 30 \
--configfile ./${sample}_config.yaml \
--cluster "sbatch --job-name=NILES --ntasks=1 --partition=long --time=12:00:00 --mem=25000 --reservation=compute006"
但是,Snakemake抱怨的文件确实存在,如果我重新运行相同的snakefile,则会运行下一条规则,但会抱怨该下一条规则的输出。 另一个细节:我为整个文件夹(当然,我有一堆fastqs并使用另一个配置文件)运行了管道,并且除其中两个样本外,每个样本都工作正常,促使我研究样本。
您知道我为什么会收到此错误吗?
答案 0 :(得分:0)
是的@Colin,您是对的。 2个样本始终失败,并且增加等待时间参数解决了该问题。我以前将其增加到30秒,但似乎还不够。 60秒解决了这个问题。