stuber
commented
5 years ago Hi Thomas,
The message of stat summary not found is an internal message. It is not bad. Looks like everything ran as it should. The SB code came back as N/A which I thought might be an error, but it wasn’t. SB codes are grabbed by cross referencing the mbovis.org database. It’s a new pattern.
Just curious because I’ve dealt with the same pysam/samtools issue. I’ve had different pysam/samtools versions error due to shared libraries not being found. I saw this when installing within a conda environment that had a lot of programs in it. It was my general run environment which had tmux installed. My RedHat version of tmux is old (1.8). I could quickly upgrade tmux via conda to 2.7, but this caused pysam/samtools to error because of shared libraries, so I’ve learned to live with the older tmux version. When first setting up your environment where pysam failed was it in a currently active environment, or did it error from a newly created environment with only vSNP environment.yml dependencies? I’ve not had issues if a new environment is created with only the dependencies in this file, but I’d like to know if you did see the error within a newly created environment.
Tod
-- Tod Stuber Computational Biologist USDA-NVSL-VS National Veterinary Services Laboratories Ames, Iowa 515-343-6935
From: "Thomas H.A. Haverkamp" notifications@github.com Reply-To: USDA-VS/vSNP reply@reply.github.com Date: Monday, December 3, 2018 at 1:40 PM To: USDA-VS/vSNP vSNP@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [USDA-VS/vSNP] Test data output? (#5)
Hi I have installed vSNP using your instructions.
Due to an error, I had to uninstall samtools using conda since it suggested the set-up was not correct. In the processes it removed a few extra dependecies including pysam. I then installed both pysam and samtools and then I tried vSNP.py out on the mycobacterium test dataset.
That ended with this output:
runtime: 0:17:34.115335:
average_coverage: 13.8
time_stamp: 2018-12-03_20-33-19
sample_name: 13-1941
species: af
reference_sequence_name: NC_002945.4
R1size: 31.0MB
R2size: 38.8MB
allbam_mapped_reads: 286,205
genome_coverage: 99.02%
ave_coverage: 13.8
ave_read_length: 227.2
unmapped_reads: 1871
unmapped_assembled_contigs: 745
good_snp_count: 675
mlst_type: N/A
octalcode: 640013777377600
sbcode: N/A
hexadecimal_code: 68-0-5F-7E-FF-60
binarycode: 1101000000000010111111111110111111111100000
Q_ave_R1: 34.7
Q30_R1: 89.9%
Q_ave_R2: 27.4
Q30_R2: 41.4%
Path to cumulative stat summary file not found
runtime: 0:19:52.687740:
See files, vSNP has finished alignments
What does that mean, when path to stat summary is not found. Is that bad?
Thomas
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Thomieh73
Hi I have installed vSNP using your instructions.
Due to an error, I had to uninstall samtools using conda since it suggested the set-up was not correct. In the processes it removed a few extra dependecies including pysam. I then installed both pysam and samtools and then I tried vSNP.py out on the mycobacterium test dataset.
That ended with this output:
What does that mean, when path to stat summary is not found. Is that bad?
Thomas