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YeoLab / MINES

(m)6A (I)dentification Using (N)anopor(E) (S)equencing
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pybedtools.helpers.BEDToolsError, Invalid record in file #13

Open vgori opened 3 years ago

vgori commented 3 years ago

Dear MINES authors, please, help with the following pipeline issue. I used  genomic_MINES.py  command for genomic_MINES.py script run: ...~/MINES# python genomic_MINES.py --fraction_modified_plus /media/localarchive/Tombo_processing/output_filename.fraction_modified_reads.plus.wig.bed --coverage_plus /media/localarchive/Tombo_processing/output_filename.coverage.plus.bedgraph --coverage_minus /media/localarchive/Tombo_processing/output_filename.coverage.minus.bedgraph --fraction_modified_minus /media/localarchive/Tombo_processing/output_filename.fraction_modified_reads.minus.wig.bed --output /media/localarchive/Tombo_processing/MINES_output/m6A_output_IRsample.bed --ref /media/localarchive/DataRRP/Homo_sapiens.GRCh38.cdna.all.fa

It gives me the following error with the command: Traceback (most recent call last): File "genomic_MINES.py", line 233, in df=df.intersect(tmp, wb=True, wa=True) File "/home/phe.gov.uk/stanislav.polozov/miniconda3/lib/python3.6/site-packages/pybedtools/bedtool.py", line 917, in decorated     result = method(self, *args, **kwargs) File "/home/phe.gov.uk/stanislav.polozov/miniconda3/lib/python3.6/site-packages/pybedtools/bedtool.py", line 401, in wrapped     decode_output=decode_output, File "/home/phe.gov.uk/stanislav.polozov/miniconda3/lib/python3.6/site-packages/pybedtools/helpers.py", line 455, in call_bedtools     raise BEDToolsError(subprocess.list2cmdline(cmds), stderr) pybedtools.helpers.BEDToolsError: Command was:


    bedtools intersect -wb -wa -b /media/localarchive/Tombo_processing/output_filename.coverage.plus.bedgraph -a /tmp/pybedtools.cnog684_.tmp

Error message was:
Error: Invalid record in file /tmp/pybedtools.cnog684_.tmp. Record is
ENST00000008180 -1      0       12      AGACT   -13     +       .

Best regards, Veronica