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mhammell-laboratory / TEsmall

A pipeline for profiling TE-derived small RNAs
GNU General Public License v3.0
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Index error when running TEsmall with hg19 database #7

Closed olivertam closed 2 years ago

olivertam commented 3 years ago

The following error pops up when running TEsmall on a FASTQ file with hg19:

[E::idx_find_and_load] Could not retrieve index file for XYZ_multi.bam '/home/.conda/envs/TEsmall/bin/TEsmall", line 33, in <module>
    sys.exit(load_entry_point('TEsmall==1.0.0', 'console_scripts', 'TEsmall')())
  File "/home/.conda/envs/TEsmall/lib/python3.7/site-packages/TEsmall-1.0.0-py3.7.egg/TEsmall/command_line.py", line 77, in main
    annofiles.append(annotate_reads(annot_dir, args.order, multi_bam))
  File "/home/.conda/envs/TEsmall/lib/python3.7/site-packages/TEsmall-1.0.0-py3.7.egg/TEsmall/annotation.py", line 36, in annotate_reads
    f_strand = line[17]
  File "pybedtools/cbedtools.pyx", line 523, in pybedtools.cbedtools.Interval.__getitem__
IndexError: field index out of range
olivertam commented 3 years ago

The cause of this error is a corrupted file in the annotation folder of the hg19 database. This should now be fixed. It is recommended that the hg19 database should be re-downloaded either by deleting the old hg19 folder and then running TEsmall -g hg19 ..., or decompress the gzipped tar ball (available here) into the TEsmall genomes folder.