Entering edit mode
3.3 years ago
sarai
•
0
Hi everyone!
I'm new on RNA-Seq analysis and I need your help. I'm trying to merge the transcript.gtf files I got with cufflinks but when I write the following command I get an error.
Can anyone suggest me how to solve this?
Thanks so much!
cuffmerge -g Mus_musculus.GRCm38.101.gtf.gz -s Mus_musculus.GRCm38.dna.primary_assembly.fa.gz assemblies.txt
[Sat Dec 5 20:19:09 2020] Beginning transcriptome assembly merge
-------------------------------------------
[Sat Dec 5 20:19:09 2020] Preparing output location ./merged_asm/
Traceback (most recent call last):
File "/home/msmenfig/tools/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 580, in <module>
sys.exit(main())
File "/home/msmenfig/tools/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 546, in main
chrom_info = get_gtf_chrom_info(gtf, chrom_info)
File "/home/msmenfig/tools/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 476, in get_gtf_chrom_info
left = int(cols[3])
ValueError: invalid literal for int() with base 10: '9\x11\x9ei;\xb6}\xf6\xce\x08\xbe\x90\x8d;\xf8\x95\x8bS\xb5\xa6\xb3q\xb7\xf6\xcc\xea\x1fO\xcf\x9fO_9\xa9\xaa2?\x18X\xe4{\xa5\x97\x1d\xa3rRR\x9a>\x93H\xce\x82\xe3\x1b;\x12\xcf\xee)\x99\xb7`C\x9f+\x95[7\x18\x94\x8f\xe1?0\xc3.f\xa6\x90\xa5W\xf8\x15\x8a\xcb]~E\x90\x0c\xcd\x07\x0fs\xbcJ\x9dl\xc8\xd1\x82\x8c\xd9JNd\xac\x0c\x05[\xb6k\xab\x1c"\xe3\xb2\x1803`\x07M\x86$2\xb6i\x866rW\xf0WF\x9d\x05\xa7\xc4\xd8\x8bnP\x8e\xe1\xc7\x1a|\x08%V\xf74\xe9'
Please use the formatting bar (especially the
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.It looks like your input files contain weird characters. What is the output to:
Also, ensure that cuffmerge can indeed work with gzipped input files.
What do you mean with "the output to" the files?
Those are commands, not files.
It looks like there might be a problem with the GTF file. Does cuffmerge accept a gzipped GTF file? Try running
If that errors out too, try
I got this with the second command line:
And I get the directory merged_asm with these files:
I think it failed because it released the FASTA prematurely. Try re-running it, but this time gunzip the fasta file first.
I got the following. Should I assume this time it worked since I got the merged.gtf file?
Yes, I think so. More importantly, you did not get any errors. I think cuffmerge failed the last time because it cannot look for an index file when the file descriptor passed to it is a
/dev/fd/
and not an actual filename.