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bcgsc / NanoSim

Nanopore sequence read simulator
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Error in read_analysis.py #104

Closed WeijiaSu closed 3 years ago

WeijiaSu commented 3 years ago

Hi, I am trying to use the "read_analysis.py genome" and I keep getting this error, it seems that the get_primary_sam.py has some problem with the HTSeq:

Traceback (most recent call last): File "/anaconda3/bin/read_analysis.py", line 552, in main() File "/anaconda3/bin/read_analysis.py", line 416, in main alnm_ext, unaligned_length, strandness = align_genome(in_fasta, prefix, aligner, num_threads, g_alnm, ref_g) File "/anaconda3/bin/read_analysis.py", line 160, in align_genome unaligned_length, strandness = get_primary_sam.primary_and_unaligned(g_alnm, prefix) File "/gpfs/fs1/anaconda3/bin/get_primary_sam.py", line 15, in primary_and_unaligned for alnm in alignments: File "/anaconda3/lib/python3.7/site-packages/HTSeq/init.py", line 854, in iter yield SAM_Alignment.from_pysam_AlignedSegment(pa, self.sf) File "python3/src/HTSeq/_HTSeq.pyx", line 1379, in HTSeq._HTSeq.SAM_Alignment.from_pysam_AlignedSegment AttributeError: 'NoneType' object has no attribute 'encode'

Thanks for your help. Weijia

cheny19 commented 3 years ago

Hi Weijia,

Could provide the command you used, the log file, and the version of NanoSim you used? It's hard to tell what's the problem simply with this error message.

Thanks, Chen

kmnip commented 3 years ago

The latest code in the master branch contains a bug fix for this issue, which uses pysam (instead of HTSeq) for reading SAM format files.