Error in iter_gmap_sam about cdna_cupcake

[Magdoll]

I've seen this error before and I think (I could remember wrong) it was related to incomplete SAM files or corrupt SAM alignment strings. Can you share the alignment file and input fasta privately? Others have used STAR with success before, but we can get to that issue later On Wed, Feb 22, 2017 at 2:46 PM Ian Fiddes <[email protected]> wrote: The program ran through a few thousand transcripts before getting to this: merged 1 down to 1 transcripts merged 1 down to 1 transcripts Traceback (most recent call last): File "/cluster/home/ifiddes/anaconda2/bin/collapse_isoforms_by_sam.py", line 4, in <module> __import__('pkg_resources').run_script('cupcake==2.1', 'collapse_isoforms_by_sam.py') File "/cluster/home/ifiddes/anaconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script File "/cluster/home/ifiddes/anaconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1499, in run_script File "/cluster/home/ifiddes/anaconda2/lib/python2.7/site-packages/cupcake-2.1-py2.7-linux-x86_64.egg/EGG-INFO/scripts/collapse_isoforms_by_sam.py", line 242, in <module> main(args) File "/cluster/home/ifiddes/anaconda2/lib/python2.7/site-packages/cupcake-2.1-py2.7-linux-x86_64.egg/EGG-INFO/scripts/collapse_isoforms_by_sam.py", line 190, in main for recs in iter: File "/cluster/home/ifiddes/anaconda2/lib/python2.7/site-packages/cupcake-2.1-py2.7-linux-x86_64.egg/cupcake/tofu/branch/branch_simple2.py", line 77, in iter_gmap_sam ignored_fout.write("{0}\tCoverage {1:.3f} too low.\n".format(r.qID, r.qCoverage)) ValueError: Unknown format code 'f' for object of type 'str' I saw this much earlier when I tried to use a STAR aligned SAM file, but then I looked through the code a bit and it seemed that you rely on identity and coverage metrics provided by gmap, so I used a gmap SAM. I was able to get through one dataset entirely, but then the next had this problem. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAkCbyS5tiMl7uEiFXb_i0Hsowb8Mk0Mks5rfLrWgaJpZM4MJS4r> .

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[ifiddes]

How can I do so?

[Magdoll]

You can email it to [email protected].

I looked at some old emails that had this error from someone else. They were able to fix this problem after re-running GMAP or STAR to generate a complete SAM. Before emailing it to me, can you please try re-running GMAP/STAR and confirm that the SAM file is complete and try running collapse again?

[ifiddes]

I figured it out. There were unmapped reads present in the SAM. To fix it, since you need sorted SAM anyways, I did the following:

samtools view -b -F 4 chimp.sam.redo | sambamba sort -o /dev/stdout /dev/stdin | samtools view - > chimp.sam.redo.sorted