hi i meet some trouble in snakemake --cores 8
Issue #71
new
the issue shows that:
- **Error in rule mageck_count:
- jobid: 3
- output: results/count/all.count.txt, results/count/all.count_normalized.txt, results/count/all.countsummary.txt
- log: logs/mageck/count/all.log (check log file(s) for error message)
- shell:
- mageck count --output-prefix results/count/all --norm-method median --list-seq pnas.1908155116.sd02.csv --fastq fastq_FOXA1_day28/SRR6749579.1.fastq fastq_FOXA1_day28/SRR6749581.1.fastq --sample-label SRR6749579.1,SRR6749581.1 --count-pair False --trim-5 AUTO 2> logs/mageck/count/all.log
- (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)**
and the log file shows that:
- **INFO @ Thu, 08 Apr 2021 20:28:11: Parameters: /cluster/huanglab/sluo/sluoo/conda/env/mageck-vispr/bin/mageck count --output-prefix results/count/all --norm-method median --list-seq pnas.1908155116.sd02.csv --fastq fastq_FOXA1_day28/SRR6749579.1.fastq fastq_FOXA1_day28/SRR6749581.1.fastq --sample-label SRR6749579.1,SRR6749581.1 --count-pair False --trim-5 AUTO
- INFO @ Thu, 08 Apr 2021 20:28:11: Welcome to MAGeCK v0.5.9.4. Command: count
- Traceback (most recent call last):
- File "/cluster/huanglab/sluo/sluoo/conda/env/mageck-vispr/bin/mageck", line 66, in <module>
- main();
- File "/cluster/huanglab/sluo/sluoo/conda/env/mageck-vispr/bin/mageck", line 47, in main
- mageckcount_main(args);
- File "/cluster/huanglab/sluo/sluoo/conda/env/mageck-vispr/lib/python3.7/site-packages/mageck/mageckCount.py", line 544, in mageckcount_main
- genedict=mageckcount_checkargs(args) # return: {sgrnaid:(seq,geneid)}
- File "/cluster/huanglab/sluo/sluoo/conda/env/mageck-vispr/lib/python3.7/site-packages/mageck/mageckCount.py", line 76, in mageckcount_checkargs
- genedict=mageckcount_checklists(args) # sgid:(seq,gene)
- File "/cluster/huanglab/sluo/sluoo/conda/env/mageck-vispr/lib/python3.7/site-packages/mageck/mageckCount.py", line 263, in mageckcount_checklists
- for line in open(args.list_seq):
- File "/cluster/huanglab/sluo/sluoo/conda/env/mageck-vispr/lib/python3.7/codecs.py", line 322, in decode
- (result, consumed) = self._buffer_decode(data, self.errors, final)
- UnicodeDecodeError: 'utf-8' codec can't decode byte 0x87 in position 10: invalid start byte** *