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miRTop / mirtop

command lines tool to annotate miRNAs with a standard mirna/isomir naming
https://mirtop.readthedocs.org
MIT License
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error when running mirtop gff example tesing #81

Closed ylang0825 closed 2 months ago

ylang0825 commented 2 months ago

Hello, I encountered a problem when running the example tesing of mirtop gff function.

I run the mirtop gff as indicated in quick start manual. Here is my code: $mirtop gff --sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out examples/annotate/sim_isomir_sort.bam

Below is the error presented: ['gff', '--sps', 'hsa', '--hairpin', 'examples/annotate/hairpin_temp.fa', '--gtf', 'examples/annotate/hsa.gff3', '-o', 'test_out', 'examples/annotate/sim_isomir_sort.bam'] 06/07/2024 09:34:27 INFO Run annotation 06/07/2024 09:34:27 INFO Reading examples/annotate/sim_isomir_sort.bam 06/07/2024 09:34:27 INFO error at command Traceback (most recent call last): File "/storeData/home/liujunfeng/miniforge3/bin/mirtop", line 8, in sys.exit(main()) File "/storeData/home/liujunfeng/miniforge3/lib/python3.10/site-packages/mirtop/command_line.py", line 31, in main reader(kwargs["args"]) File "/storeData/home/liujunfeng/miniforge3/lib/python3.10/site-packages/mirtop/gff/init.py", line 45, in reader reads = _read_bam(fn, args) File "/storeData/home/liujunfeng/miniforge3/lib/python3.10/site-packages/mirtop/gff/init.py", line 94, in _read_bam reads = read_bam(bam_fn, precursors) File "/storeData/home/liujunfeng/miniforge3/lib/python3.10/site-packages/mirtop/bam/bam.py", line 46, in read_bam bam_fn = _bam_sort(bam_fn) File "/storeData/home/liujunfeng/miniforge3/lib/python3.10/site-packages/mirtop/bam/bam.py", line 332, in _bam_sort do.run(("samtools sort -n -o {bam_sort_by_n} {bam_fn}").format( File "/storeData/home/liujunfeng/miniforge3/lib/python3.10/site-packages/mirtop/libs/do.py", line 20, in run _do_run(cmd, checks, log_stdout) File "/storeData/home/liujunfeng/miniforge3/lib/python3.10/site-packages/mirtop/libs/do.py", line 79, in _do_run error_msg += "".join(debug_stdout) TypeError: sequence item 0: expected str instance, bytes found

Could you please help me find out where the problem is? Thank you very much.

ylang0825 commented 2 months ago

I found this was because I did not activate the virtual enrivonment. Done already.