Error in STAR's bams when running ht-seq

Question

[greener]

Hi I am using the newest version of star that generated sorted bams and attempting to generate counts using ht-seq. STAR creates the bams successfully but when I try to run ht-seq it generates the following error (below). Any suggestions folks have is appreciated. Thanks -Rich

STAR command;

/vol01/ngs_tools/mapper/STAR-STAR_2.4.0h1/source/STAR \
  --genomeDir /vol01/genome/vervet_AGM_pre_release/ens78/ \
  --clip5pNbases 1 \
  --clip3pNbases 1 \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --readFilesIn file1_nohmrRNA_1.fastq.gz file2_nohmrRNA_2.fastq.gz \
  --outFileNamePrefix path/agm_file \
  --runThreadN 15

Then HT-seq command:

/vol01/ngs_tools/python/install/Python-2.7.3/bin/htseq-count \
  --stranded=yes \
  --mode=intersection-nonempty \
  --idattr=gene_id \
  --order=pos \
  ACGTCCTG.AGCTTCAG_8Aligned.sortedByCoord.out.bam \
  /vol01/genome/vervet_AGM_pre_release/ChlSab1.1.genes.gtf > /path/ACGTCCTG.AGCTTCAG_8_agm_1.1.counts.txt

Output/Error:

100000 GFF lines processed.
200000 GFF lines processed.
300000 GFF lines processed.
400000 GFF lines processed.
414614 GFF lines processed.
ERROR:root:code for hash md5 was not found.
Traceback (most recent call last):
  File "/vol01/ngs_tools/python/install/Python-2.7.3/lib/python2.7/hashlib.py", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/vol01/ngs_tools/python/install/Python-2.7.3/lib/python2.7/hashlib.py", line 91, in __get_builtin_constructor
    raise ValueError('unsupported hash type %s' % name)
ValueError: unsupported hash type md5

Answer 1

[Sean Davis]

This probably has nothing to do with aligning using STAR. Unfortunately, it appears that your python 2.7 hashlib is probably broken. It is hard to tell why, but a google search for "ValueError: unsupported hash type md5" turns up a few ideas.