PySam issue

[francoissabot]

Hi folks

i installed the last version of blobtools, and have an unexpected issue with Pysam use:

here are my commands and outputs

$ ~/sources/blobtools/blobtools create -i flyeAsmComplete/scaffolds.fasta -b flyeAsmComplete/scaffolds.fasta.Illumina.sam.bam.SORTED.bam --db ~/sources/blobtools/data/nodesDB.txt -t flye_blast_alignement.tsv -o flye_blobtools [+] Parsing FASTA - flyeAsmComplete/scaffolds.fasta [+] names.dmp/nodes.dmp not specified. Retrieving nodesDB from /home/xxxx/sources/blobtools/data/nodesDB.txt [%] : 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.09M/2.09M [00:07<00:00, 267kit/s] [+] Parsing tax0 - /Data/rufipogon/AssemblyW1654/flye_blast_alignement.tsv [+] Computing taxonomy using taxrule(s) bestsum [%] : 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4.30k/4.30k [00:06<00:00, 666it/s] [+] Parsing bam0 - /Data/rufipogon/AssemblyW1654/flyeAsmComplete/scaffolds.fasta.Illumina.sam.bam.SORTED.bam [+] -> 100.00 (4297/4297) of sequences have reads aligned to them. [+] -> 99.36 (98958700/99594253) of reads are mapped. [%] : 0%| | 0.00/4.30k [00:00<?, ?it/s] Traceback (most recent call last): File "/home/xxxx/sources/blobtools/blobtools", line 7, in main() File "/home/xxxx/Documents/sources/blobtools/lib/interface.py", line 60, in main create.main() File "/home/xxxx/Documents/sources/blobtools/lib/create.py", line 119, in main blobDb.parseCoverage(covLibObjs=cov_libs, estimate_cov=estimate_cov_flag, prefix=prefix) File "/home/xxxx/Documents/sources/blobtools/lib/BtCore.py", line 369, in parseCoverage base_cov_dict, covLib.reads_total, covLib.reads_mapped, read_cov_dict = BtIO.parseBam(covLib.f, set(self.dict_of_blobs), estimate_cov) File "/home/xxxx/Documents/sources/blobtools/lib/BtIO.py", line 224, in parseBam base_cov_dict, read_cov_dict = estimate_coverage(aln, set_of_blobs) File "/home/xxxx/Documents/sources/blobtools/lib/BtIO.py", line 235, in estimate_coverage read_count = aln.count(header, read_callback=check_mapped_read) File "pysam/calignmentfile.pyx", line 1081, in pysam.calignmentfile.AlignmentFile.count TypeError: count() got an unexpected keyword argument 'read_callback'

Any idea ? My pysam are up to date, my python 3 version is 3.5.2, my system ubuntu 16.04

[DRL]

Hi,

could it be that the BAM is not indexed?

cheers,

dom

[francoissabot]

The bam is indexed :

$ ls flyeAsmComplete/scaffolds.fasta.Illumina.sam.bam.SORTED.bam* flyeAsmComplete/scaffolds.fasta.Illumina.sam.bam.SORTED.bam flyeAsmComplete/scaffolds.fasta.Illumina.sam.bam.SORTED.bam.bai

[DRL]

Hmm, weird ...

the changelog of pysam says that read_callback function of count was implemented in Release 0.9.0, which also requires htslib 1.3

did you install the dependencies via conda? could you check that you have those versions or newer on your system?

cheers,

dom

[francoissabot]

I have installed everything through pip.. I am testing through Conda by now

[francoissabot]

Ok, working in pure conda...