Closed ShriramHPatel closed 8 years ago
Hi Shriram, What happens when you run anvi-self-test
?
Hello,
I ran anvi-self-test and it completed succesfully. I used this in past many times, but never ran into such error. I did the following things in step by step manner, hope it can help.
Parallely,
Now, I am runnin avni-profile for individual samples.
Thank You
Hi,
Steps you followed make sense to me, and ifanvi-self-test
is running without any errors, this is not a problem related to anvi'o or your system :/ I would look into the mapping results more carefully.
One or more of your BAM files may have no aligned reads in it (regardless of the size of the file), but I am not sure.
Best,
Hello,
I am getting following Error on running anvio-profile command:
[E::bam_hdr_read] error reading BGZF stream Traceback (most recent call last): File "/usr/local/bin/anvi-profile", line 68, in <module> profiler._run() File "/usr/local/lib/python2.7/dist-packages/anvio/profiler.py", line 192, in _run self.profile() File "/usr/local/lib/python2.7/dist-packages/anvio/profiler.py", line 651, in profile contig.analyze_auxiliary(self.bam, self.progress) File "/usr/local/lib/python2.7/dist-packages/anvio/contigops.py", line 120, in analyze_auxiliary report_variability_full=self.report_variability_full) File "/usr/local/lib/python2.7/dist-packages/anvio/contigops.py", line 165, in __init__ self.run(bam) File "/usr/local/lib/python2.7/dist-packages/anvio/contigops.py", line 171, in run for pileupcolumn in bam.pileup(self.split.parent, self.split.start, self.split.end): File "pysam/calignmentfile.pyx", line 1105, in pysam.calignmentfile.AlignmentFile.pileup (pysam/calignmentfile.c:11743) File "pysam/calignmentfile.pyx", line 2304, in pysam.calignmentfile.IteratorColumnRegion.__cinit__ (pysam/calignmentfile.c:23147) File "pysam/calignmentfile.pyx", line 2209, in pysam.calignmentfile.IteratorColumn.setupIteratorData (pysam/calignmentfile.c:22204) File "pysam/calignmentfile.pyx", line 1746, in pysam.calignmentfile.IteratorRowRegion.__init__ (pysam/calignmentfile.c:17915) File "pysam/calignmentfile.pyx", line 1703, in pysam.calignmentfile.IteratorRow.__init__ (pysam/calignmentfile.c:17529) AssertionError
I am using anvio-2.0.2.
I used following command:
anvio-profile -i 1-1.bam -c contigs.db -M 2000 -S Sample1-1 -o 1-1/
Can I get any help on this? I am unaware of Assertion Error.
Thank You,
Regards Shriram