kerenzhou062 / peals Goto Github PK

(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. 

-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)