iqbal-lab
commented
7 years ago What precise version of predictor are you using - did you get it from github? Do you have a commit number? How did you install , and has it worked for you before?
Closed harrismia closed 5 years ago
iqbal-lab
commented
7 years ago What precise version of predictor are you using - did you get it from github? Do you have a commit number? How did you install , and has it worked for you before?
harrismia
commented
7 years ago Hi,
We did get if from github. For the linux version: typing mykrobe --version gives : mykrobe v0.5.6-0-gbd7923a-dirty
The same command on my Mac Book Pro gives: mykrobe v0.5.1-0-g04fef92 I see that they are different. I have been using the version on my Mac Book but we have never tried using it on our linux cluster before.
I didn't do the install on the linux cluster so I will find out the details and respond. Thanks,
Michael
Phelimb
commented
7 years ago @harrismia Could you upload the output of pip freeze when run within your virtualenv ? This looks like the version of mykatlas is incompatible with the version of mykrobe.
Phelimb
commented
7 years ago It looks like the local install of mccortex seems to fail with anaconda venvs. You might need to reinstall mccortex.
git clone --recursive https://github.com/iqbal-lab/Mykrobe-predictor.git
cd Mykrobe-predictor
cd mccortex
make
export PATH=$(pwd)/bin:$PATH
cd ..The version should read:
mccortex31 --version
mccortex=v0.0.3-482-g22410eaDear Mykrobe-predictor support team:
I have recompiled mccortex31 and copied the executable under mykrobe’s bin folder. Sadly, “mykrobe predict” still fails. I wonder if “mykatlas==0.6.1” is an incorrect version. Will wait for comments from Phelim Bradley (please forward his reply to me). Thanks!
» mccortex31 --version
Error: Unrecognised command: --version
usage: mccortex31
Commands: breakpoints use a trusted assembled genome to call large events
bubbles find bubbles in graph which are potential variants
build construct cortex graph from FASTA/FASTQ/BAM
calls2vcf convert bubble/breakpoint calls to VCF
check load and check graph (.ctx) and path (.ctp) files
clean clean errors from a graph
contigs assemble contigs for a sample
correct error correct reads
coverage print contig coverage
dist make colour kmer distance matrix
index index a sorted cortex graph file
inferedges infer graph edges between kmers before calling thread
join combine graphs, filter graph intersections
links clean and plot link files (.ctp)
pjoin merge path files (.ctp)
popbubbles pop bubbles in the population graph
pview text view of a cortex path file (.ctp)
reads filter reads against a graph
rmsubstr reduce set of strings to remove substrings
server interactively query the graph
sort sort the kmers in a graph file
subgraph filter a subgraph using seed kmers
thread thread reads through cleaned graph to make links
uniqkmers generate random unique kmers
unitigs pull out unitigs in FASTA, DOT or GFA format
vcfcov coverage of a VCF against cortex graphs
vcfgeno genotype a VCF after running vcfcov
view text view of a cortex graph file (.ctx)
Type a command with no arguments to see help.
Common Options:
-h, --help Help message
-q, --quiet Silence status output normally printed to STDERR
-f, --force Overwrite output files if they already exist
-m, --memory
/sysapps/cluster/modules/all/mykrobe/0.5.6-Python-3.5:
(mykrobeenv) appbuild@ai-submit1» ls /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/bin 2to3 easy_install mykrobe pydoc3.5 python3-config vcf_melt 2to3-3.5 easy_install-3.5 openssl python pyvenv vcf_sample_filter.py activate f2py pasteurize python3 pyvenv-3.5 wheel atlas futurize pip python3.5 sqlite3 wish8.5 conda idle3 pycache python3.5-config tclsh8.5 xz c_rehash idle3.5 pydoc python3.5m unxz deactivate mccortex31 pydoc3 python3.5m-config vcf_filter.py
(mykrobeenv) appbuild@ai-submit1» which mccortex31 ~/eb_files/Mykrobe-predictor/Mykrobe-predictor/mccortex/bin/mccortex31
(mykrobeenv) appbuild@ai-submit1» cp ~/eb_files/Mykrobe-predictor/Mykrobe-predictor/mccortex/bin/mccortex31 /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/bin/.
(mykrobeenv) appbuild@ai-submit1» mykrobe predict SRR5486866 tb --seq /hpcdata/bcbb/tbportal/genomics/SequencingCenterDownloads/Borstel/Romania_50samples/TBprofiler/SRR5486866_1.fastq.gz
INFO:root:Running AMR prediction with panels data/panels/tb-species-170421.fasta.gz, data/panels/tb-walker-probe-set-feb-09-2017.fasta.gz
Traceback (most recent call last):
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/bin/mykrobe", line 11, in
Reply:
It looks like the local install of mccortex seems to fail with anaconda venvs. You might need to reinstall mccortex.
git clone --recursive https://github.com/iqbal-lab/Mykrobe-predictor.git
cd Mykrobe-predictor
cd mccortex
make
export PATH=$(pwd)/bin:$PATH
cd ..The version should read:
mccortex31 --version
mccortex=v0.0.3-482-g22410ea
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/iqbal-lab/Mykrobe-predictor/issues/126#issuecomment-317187026, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AcVozLGHuFIfOMK3INe7k7WJ-d4JBvbWks5sQgaqgaJpZM4OdKvy.
iqbal-lab
commented
7 years ago I'm just going on holiday, so will ping @Phelimb
noporpoise
commented
7 years ago Looks like Mykrobe-predictor should be using the McCortex vcfgeno command instead of geno.
Phelimb
commented
7 years ago So, I have a branch of mccortex where geno is a valid command that should work with Mykrobe predictor.
https://github.com/phelimb/mccortex/tree/genotype
I'm not 100% sure what's causing this error but it seems to be a version clash between mccortex, or mykaltlas.
You have the correct mykatlas but the mccortex version should be v0.0.3-481-gbbe4edf-dirty
Which you can get manually by running
git clone -b genotype https://github.com/phelimb/mccortex
joshualoving
commented
7 years ago When I compile https://github.com/phelimb/mccortex/tree/genotype, I get the same version number mccortex=v0.0.3-482-g22410ea, not v0.0.3-481-gbbe4edf-dirty
Hello,
mykrobe predict SRR5486866 tb --seq ./SRR5486866_1.fastq.gz INFO:root:Running AMR prediction with panels data/panels/tb-species-170421.fasta.gz, data/panels/tb-walker-probe-set-feb-09-2017.fasta.gz Traceback (most recent call last): File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/bin/mykrobe", line 11, in
sys.exit(main())
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 125, in main
args.func(parser, args)
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 34, in run_subtool
run(parser, args)
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykrobe/cmds/amr.py", line 134, in run
cp.run()
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 74, in run
self._parse_covgs()
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 128, in _parse_covgs
row)
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 118, in _parse_summary_covgs_row
return row[0], int(row[2]), int(row[3]), 100 * float(row[4]), int(row[5])
IndexError: list index out of range