Cuffmerge error while merging gtf files

Question

[AP]

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

[GenoMax]

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.

[AP]

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

[AP]

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