Question: Cuffmerge error while merging gtf files
0
gravatar for Ambika
21 months ago by
Ambika30
United States/Auburn/Auburn University
Ambika30 wrote:

Hi everyone,

I was trying to merge my transcripts.gtf files from cufflinks using cuffmerge but i am getting bunch of errors. SCRIPT:

cuffmerge -s Fov89-1A_65_contigs.fasta -o cuffmerge_output assembly_list.txt

ERROR:

ERROR:root:code for hash md5 was not found.
Traceback (most recent call last):
  File "/opt/asn/apps/python_2.7.3/lib/python2.7/hashlib.py", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/asn/apps/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
ERROR:root:code for hash sha1 was not found.
Traceback (most recent call last):
  File "/opt/asn/apps/python_2.7.3/lib/python2.7/hashlib.py", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/asn/apps/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 sha1
ERROR:root:code for hash sha224 was not found.
Traceback (most recent call last):
  File "/opt/asn/apps/python_2.7.3/lib/python2.7/hashlib.py", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/asn/apps/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 sha224
ERROR:root:code for hash sha256 was not found.
Traceback (most recent call last):
  File "/opt/asn/apps/python_2.7.3/lib/python2.7/hashlib.py", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/asn/apps/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 sha256
ERROR:root:code for hash sha384 was not found.
Traceback (most recent call last):
  File "/opt/asn/apps/python_2.7.3/lib/python2.7/hashlib.py", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/asn/apps/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 sha384
ERROR:root:code for hash sha512 was not found.
Traceback (most recent call last):
  File "/opt/asn/apps/python_2.7.3/lib/python2.7/hashlib.py", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/opt/asn/apps/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 sha512

[Tue Oct 10 11:45:04 2017] Beginning transcriptome assembly merge
-------------------------------------------

[Tue Oct 10 11:45:04 2017] Preparing output location cuffmerge_output/
Warning: no reference GTF provided!
[Tue Oct 10 11:45:06 2017] Converting GTF files to SAM
[11:45:06] Loading reference annotation.
[11:45:07] Loading reference annotation.
[11:45:08] Loading reference annotation.
[11:45:09] Loading reference annotation.
[11:45:09] Loading reference annotation.
[11:45:10] Loading reference annotation.
[11:45:11] Loading reference annotation.
[11:45:12] Loading reference annotation.
[Tue Oct 10 11:45:13 2017] Assembling transcripts
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Command line:
cufflinks -o cuffmerge_output/ -F 0.05 -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 1 cuffmerge_output/tmp/mergeSam_file6rQ8VX
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File cuffmerge_output/tmp/mergeSam_file6rQ8VX doesn't appear to be a valid BAM file, trying SAM...
[11:45:13] Inspecting reads and determining fragment length distribution.
Processed 7284 loci.
> Map Properties:
>       Normalized Map Mass: 87951.00
>       Raw Map Mass: 87951.00
>       Fragment Length Distribution: Truncated Gaussian (default)
>                     Default Mean: 200
>                  Default Std Dev: 80
[11:45:15] Assembling transcripts and estimating abundances.
Processed 7284 loci.
[Tue Oct 10 11:46:02 2017] Comparing against reference file None
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
[Tue Oct 10 11:46:05 2017] Comparing against reference file None
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).

But I am getting the output file merged.gtf out of it. I dont know how.

Please help me, Thank you, Ambika

cuffmerge rna-seq • 751 views
ADD COMMENTlink modified 21 months ago by genomax70k • written 21 months ago by Ambika30

This appears to be an error with installation of OpenSSL libraries and python (ref ). If you are not the administrator of this machine report this to the sys admin.

ADD REPLYlink written 21 months ago by genomax70k

I did that , and waiting for their reply. Do you have any idea why am I getting the output files though.

ADD REPLYlink written 21 months ago by Ambika30

They said they will install new cufflinks and it might take week or two.. Already spend lots of time trying this and that do you know any alternatives

ADD REPLYlink written 21 months ago by Ambika30
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