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View Code? Open in Web Editor NEWPeak-based Enhancement Analysis pipeLine for MeRIP-Seq
License: MIT License
Peak-based Enhancement Analysis pipeLine for MeRIP-Seq
License: MIT License
周老师您好,我在使用peals callpeak时出现几个问题
第一个错误如下:
(python38) root@1ef77f50eaef:/file# peals callpeak -i . -m PEALS/example/peals.callpeak.sample.txt -P peals -o peals \
> --gsize /file/hg38.chrom.sizes \
> --gff /file/Homo_sapiens.GRCh38.91.gtf \
> --gff-type GTF
INFO @ Wed, 23 Aug 2023 14:21:42: PEALS (v1.2.4) is running with following parameters:
INFO @ Wed, 23 Aug 2023 14:21:42: [input] parameter group: call-with-binary=False, binary-dir=None, input=., matrix=PEALS/example/peals.callpeak.sample.txt, recursive=False, type=mature, sample=None
INFO @ Wed, 23 Aug 2023 14:21:42: [output] parameter group: keep-temp=False, no-bwtrack=False, output=peals, prefix=peals, temp=None, verbose=2
INFO @ Wed, 23 Aug 2023 14:21:42: [library] parameter group: estlib-size=primary_mapped, extsize=0, library=2, pairend=False
INFO @ Wed, 23 Aug 2023 14:21:42: [normalize] parameter group: bw-scale=rpm, exp-method=count, estpeak-sizefactor=peak
INFO @ Wed, 23 Aug 2023 14:21:42: [bam] parameter group: exp-cutoff=1, frac-overlap=0, ignore-dup=False, no-fraction=False, scale-sample=to_small, sortbam=False
INFO @ Wed, 23 Aug 2023 14:21:42: [constant] parameter group: buffer=10000000, reltol=0.05, thread=10, thread-start=fork
INFO @ Wed, 23 Aug 2023 14:21:42: [annotation] parameter group: gff=/file/Homo_sapiens.GRCh38.91.gtf, gff-source=GENCODE, gff-type=GTF, gsize=/file/hg38.chrom.sizes, identifier=gene_id:gene_name:gene_type:transcript_id:transcript_name:transcript_type
INFO @ Wed, 23 Aug 2023 14:21:42: [peak] parameter group: center=0.25, complexity-rate=0.05, csaps-p=0.005, ipratio=1.25, lookahead=25, peak-size=35, span-loop=1, span-method=move, split=50000
INFO @ Wed, 23 Aug 2023 14:21:42: [model] parameter group: fit-type=parametric, formula=None, shrink=apeglm, test=Wald
INFO @ Wed, 23 Aug 2023 14:21:42: [filter] parameter group: fold=2, padj=0.05, padj-method=BH, pval=0.05
INFO @ Wed, 23 Aug 2023 14:21:42: Checking whether required third party software are properly installed...
INFO @ Wed, 23 Aug 2023 14:21:42: Congratulations! All required third party software are properly installed!
Traceback (most recent call last):
File "/root/.local/bin/peals", line 352, in <module>
main()
File "/root/.local/bin/peals", line 35, in main
run( args )
File "/root/.local/lib/python3.8/site-packages/PEALS/subcmd/callpeak_cmd.py", line 51, in run
tempPrefix = os.path.join(options.tempdir, "_".join([options.tempre, options.prefix]))
File "/root/mambaforge-pypy3/envs/python38/lib/python3.8/posixpath.py", line 76, in join
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType
INFO @ Wed, 23 Aug 2023 14:21:42: Embedded R ended.
INFO @ Wed, 23 Aug 2023 14:21:42: Embedded R already ended.
经过检查options后,确实发现options.tempdir=None ,使用-T参数即可解决这个问题
值得一提,在help内,有以下说明
-o OUTPUTDIR, --output OUTPUTDIR
All output files will be written to this directory. (default: None)
-T TEMPDIR, --temp TEMPDIR
If specified, all temporary files will be written to this directory. Default is the same with --output.
(default: None)
说明上写的是默认和-o参数一致,但实际上没有一致,可能是老师您漏掉了这个地方。
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