I'm also receiving the following error from another bam file:
[sam_header_read2] 84 sequences loaded. [mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Traceback (most recent call last):
File "/data/singhln/Projects/MToolBox/mt-classifier.py", line 327, in <module>
main_mt_hpred()
File "/data/singhln/Projects/MToolBox/mt-classifier.py", line 275, in main_mt_hpred
m = list(seq_classify.mhcss)[0]
IndexError: list index out of range
Here's the logassemble.txt:
/data/singhln/Projects/ES/Data/chrRCRS.fa
/data/singhln/Projects/ES/Data/human_g1k_v37_RCRS.fasta
assembleMTgenome for sample CS171401
Converting SAM to BAM...
Sorting and indexing BAM...
Creating pileup...
Reading mtDNA sequence...
Reading pileup file...
Assembling...
Basic statistics:
Assembled bases: 1.82%
Mean coverage depth: 5.50
Number of Contigs: 13
Base composition [A,C,G,T]: 0.00,0.01,0.00,0.00
searching for indels in CS171401_TruSeqV2.. please wait...
searching for mismatches in CS171401_TruSeqV2.. please wait...
Any help appreciated. Grazie mille.
-Larry.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
thanks for this alert. We will be working on it as soon as possible, you're giving us many though nuts to crack :) (and we appreciate it a lot, of course!).
We'll get back to you soon!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I'm also receiving the following error from another bam file:
[sam_header_read2] 84 sequences loaded.
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Traceback (most recent call last):
File "/data/singhln/Projects/MToolBox/mt-classifier.py", line 327, in <module>
main_mt_hpred()
File "/data/singhln/Projects/MToolBox/mt-classifier.py", line 275, in main_mt_hpred
m = list(seq_classify.mhcss)[0]
IndexError: list index out of range
Here's the logassemble.txt:
/data/singhln/Projects/ES/Data/chrRCRS.fa
/data/singhln/Projects/ES/Data/human_g1k_v37_RCRS.fasta
assembleMTgenome for sample CS171401
Converting SAM to BAM...
Sorting and indexing BAM...
Creating pileup...
Reading mtDNA sequence...
Reading pileup file...
Assembling...
Basic statistics:
Assembled bases: 1.82%
Mean coverage depth: 5.50
Number of Contigs: 13
Base composition [A,C,G,T]: 0.00,0.01,0.00,0.00
searching for indels in CS171401_TruSeqV2.. please wait...
searching for mismatches in CS171401_TruSeqV2.. please wait...
Any help appreciated. Grazie mille.
-Larry.
Dear Larry,
thanks for this alert. We will be working on it as soon as possible, you're giving us many though nuts to crack :) (and we appreciate it a lot, of course!).
We'll get back to you soon!
Caro Domenico,
Grazie mille. I appreciate all your hard and good work. Rest assured, I'm using MToolBox extensively. :)
A presto!
-Larry.