Hi everyone,
I am using HTSeq 0.4.7 on a Mac OS X with Python 2.7 and Numpy 1.5.1.
It's my first time using the program, and I am getting a strange error.
After calling the htseq-counts script using:
>python -m HTSeq.scripts.count -a 1 polyA_sorted.sam Homo_sapiens.GRCh37.61.gtf
I get the following error:
Error occured in line 2196 of file ../../data/htseq_count/polyA_sorted.sam.
Error:
[Exception type: AssertionError, raised in __init__.py:576]
"polyA_sorted.sam" contains paired-end reads mapped using bwa and sorted by read name, and "Homo_sapiens.GRCh37.61.gtf" is the latest GTF file from Ensembl.
Line 2196 and 2197 of polyA_sorted.sam are:
DBBK90L1:8:1:10101:43720#0 145 22 50502479 37 97M = 50499957 -2619 TCCTGCGGGCCGTTCTGGGTGTCCCAGGATGCACCCTGCAGCCTTGCACTGACCTTGAAGCGCACGCACTGGATGGCGGTGCCCGTGTTGAGGCCGG BBBBBBBBBBBBBBBB`bccX[b^bcecd`debZcddead_gefdedbf_daeZddgbdegbg`eedbdgggcegebbgggeggggggggggggggg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:97
DBBK90L1:8:1:10101:43720#0 97 22 50499957 37 97M = 50502479 2619 GTTTCCATGCCTGGGGCCAGGCTGGGCGCTGCCACCCGGTTTCCGCGTCTGGGGGTCACTGGGCCATTTGCACCACGACGGCTCTCCAGGCTTTCTC gggeggggggggggggggfggggggfggfggggadgggceeeeegggdedacbe`Gbb^`X^bZcbdddd^ggdgeg`gddeeedbdc_V`M```ca XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T86
I'm thoroughly confused about what is causing this error, and I would appreciate any help with this problem. Thank you!
Cheers,
Sandy
I am using HTSeq 0.4.7 on a Mac OS X with Python 2.7 and Numpy 1.5.1.
It's my first time using the program, and I am getting a strange error.
After calling the htseq-counts script using:
>python -m HTSeq.scripts.count -a 1 polyA_sorted.sam Homo_sapiens.GRCh37.61.gtf
I get the following error:
Error occured in line 2196 of file ../../data/htseq_count/polyA_sorted.sam.
Error:
[Exception type: AssertionError, raised in __init__.py:576]
"polyA_sorted.sam" contains paired-end reads mapped using bwa and sorted by read name, and "Homo_sapiens.GRCh37.61.gtf" is the latest GTF file from Ensembl.
Line 2196 and 2197 of polyA_sorted.sam are:
DBBK90L1:8:1:10101:43720#0 145 22 50502479 37 97M = 50499957 -2619 TCCTGCGGGCCGTTCTGGGTGTCCCAGGATGCACCCTGCAGCCTTGCACTGACCTTGAAGCGCACGCACTGGATGGCGGTGCCCGTGTTGAGGCCGG BBBBBBBBBBBBBBBB`bccX[b^bcecd`debZcddead_gefdedbf_daeZddgbdegbg`eedbdgggcegebbgggeggggggggggggggg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:97
DBBK90L1:8:1:10101:43720#0 97 22 50499957 37 97M = 50502479 2619 GTTTCCATGCCTGGGGCCAGGCTGGGCGCTGCCACCCGGTTTCCGCGTCTGGGGGTCACTGGGCCATTTGCACCACGACGGCTCTCCAGGCTTTCTC gggeggggggggggggggfggggggfggfggggadgggceeeeegggdedacbe`Gbb^`X^bZcbdddd^ggdgeg`gddeeedbdc_V`M```ca XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T86
I'm thoroughly confused about what is causing this error, and I would appreciate any help with this problem. Thank you!
Cheers,
Sandy
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