Question: Error in STAR's bams when running ht-seq
gravatar for greener
4.2 years ago by
United States
greener10 wrote:

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



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/", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/vol01/ngs_tools/python/install/Python-2.7.3/lib/python2.7/", line 91, in __get_builtin_constructor
    raise ValueError('unsupported hash type %s' % name)
ValueError: unsupported hash type md5


ADD COMMENTlink modified 4.2 years ago by Sean Davis25k • written 4.2 years ago by greener10
gravatar for Sean Davis
4.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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.

ADD COMMENTlink written 4.2 years ago by Sean Davis25k
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