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Spades version detection error #67

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uranus2001 opened this issue Aug 5, 2016 · 10 comments

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@uranus2001
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commented Aug 5, 2016

I just installed Circlator version: 1.2.1 using pip3 on my mac (OS X El Captain) after installing all the dependencies in the correct versions (I believe), but when I run progcheck, it gives me an error: Found spades but couldn't get version. Any suggestions to solve this issue? Thanks!

Below is the output when I type in "circlator progcheck".

Circlator version: 1.2.1

External dependencies:
bwa 0.7.15 xxxxxx
nucmer 3.1 xxxxxx
prodigal 2.6.3 xxxxxx
samtools 1.3.1 xxxxxx
Found spades but couldn't get version.

Python version:
3.5.2 (v3.5.2:4def2a2901a5, Jun 26 2016, 10:47:25)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]

Python dependencies:
bio_assembly_refinement 0.5.1 /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/bio_assembly_refinement/init.py
openpyxl 2.3.5 /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/openpyxl/init.py
pyfastaq 3.12.1 /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/pyfastaq/init.py
pymummer 0.7.1 /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/pymummer/init.py
pysam 0.8.3 /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/pysam/init.py

@martinghunt

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commented Aug 5, 2016

What version of spades do you have installed? I haven't tested circlator with the newest versions. It definitely works with spades 3.6.0.

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commented Aug 5, 2016

I tried all 3.5.0 / 3.6.0 / 3.6.2, but none of them was detected by Circlator. I tested Spades itself, and it is working okay.

@martinghunt

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commented Aug 5, 2016

Does

python2 spades.py

work? (Replace spades.py with full path to where it is on your system)

@uranus2001

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commented Aug 5, 2016

Sorry for the confusion with my previous reply. I typed in the Spades executable earlier rather than .py script.

Now, with python spades.py(full path), it gives me basically "help" print with all the options.

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commented Aug 8, 2016

Can you paste the output of

python2 `which spades.py`
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commented Aug 8, 2016

xxxxxx:~ jungh$ which spades.py
(Return)
/xxxxxx/TIS/SPAdes-3.6.0-Darwin/bin/spades.py

I tried two different mac (OS X 10.9.5 & 10.11.4) computers without success (the same Spades version detection problem), but it worked okay with BioLinux computers in the lab. So, now I guess this might relate to platforms??

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commented Aug 8, 2016

Could you confirm what the output is of the complete command

python2 `which spades.py`

on your mac? We tested it here on OSX 10.11.6 and it worked. Also, how are you installing spades?

@uranus2001

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commented Aug 8, 2016

I believe I got SPAdes binaries for Mac though curl and for linux through wget.
curl http://spades.bioinf.spbau.ru/release3.6.0/SPAdes-3.6.0-Darwin.tar.gz -o SPAdes-3.6.0-Darwin.tar.gz
wget http://spades.bioinf.spbau.ru/release3.6.0/SPAdes-3.6.0-Linux.tar.gz

Here is the output of the complete command. Thanks!

xxxxxx:~ jungh$ python2 `which spades.py`
-bash: python2: command not found
xxxxxx:~ jungh$ python `which spades.py`
SPAdes genome assembler v.3.6.0

Usage: /xxxxxx/TIS/SPAdes-3.6.0-Darwin/bin/spades.py [options] -o <output_dir>

Basic options:
-o  <output_dir>    directory to store all the resulting files (required)
--sc            this flag is required for MDA (single-cell) data
--iontorrent        this flag is required for IonTorrent data
--test          runs SPAdes on toy dataset
-h/--help       prints this usage message

Input data:
--12    <filename>  file with interlaced forward and reverse paired-end reads
-1  <filename>  file with forward paired-end reads
-2  <filename>  file with reverse paired-end reads
-s  <filename>  file with unpaired reads
--pe<#>-12  <filename>  file with interlaced reads for paired-end library number <#> (<#> = 1,2,3,4,5)
--pe<#>-1   <filename>  file with forward reads for paired-end library number <#> (<#> = 1,2,3,4,5)
--pe<#>-2   <filename>  file with reverse reads for paired-end library number <#> (<#> = 1,2,3,4,5)
--pe<#>-s   <filename>  file with unpaired reads for paired-end library number <#> (<#> = 1,2,3,4,5)
--pe<#>-<or>    orientation of reads for paired-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
--s<#>      <filename>  file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)
--mp<#>-12  <filename>  file with interlaced reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
--mp<#>-1   <filename>  file with forward reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
--mp<#>-2   <filename>  file with reverse reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
--mp<#>-s   <filename>  file with unpaired reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
--mp<#>-<or>    orientation of reads for mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
--hqmp<#>-12    <filename>  file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
--hqmp<#>-1 <filename>  file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
--hqmp<#>-2 <filename>  file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
--hqmp<#>-s <filename>  file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
--hqmp<#>-<or>  orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
--nxmate<#>-1   <filename>  file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
--nxmate<#>-2   <filename>  file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
--sanger    <filename>  file with Sanger reads
--pacbio    <filename>  file with PacBio reads
--nanopore  <filename>  file with Nanopore reads
--trusted-contigs   <filename>  file with trusted contigs
--untrusted-contigs <filename>  file with untrusted contigs

Pipeline options:
--only-error-correction runs only read error correction (without assembling)
--only-assembler    runs only assembling (without read error correction)
--careful       tries to reduce number of mismatches and short indels
--continue      continue run from the last available check-point
--restart-from  <cp>    restart run with updated options and from the specified check-point ('ec', 'as', 'k<int>', 'mc')
--disable-gzip-output   forces error correction not to compress the corrected reads
--disable-rr        disables repeat resolution stage of assembling

Advanced options:
--dataset   <filename>  file with dataset description in YAML format
-t/--threads    <int>       number of threads
                [default: 16]
-m/--memory <int>       RAM limit for SPAdes in Gb (terminates if exceeded)
                [default: 250]
--tmp-dir   <dirname>   directory for temporary files
                [default: <output_dir>/tmp]
-k      <int,int,...>   comma-separated list of k-mer sizes (must be odd and
                less than 128) [default: 'auto']
--cov-cutoff    <float>     coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
--phred-offset  <33 or 64>  PHRED quality offset in the input reads (33 or 64)
                [default: auto-detect]
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commented Aug 9, 2016

OK, so it looks like the issue is that circlator assumes that the command "python2" is in your path. I'll fix this in the next week or two and do a new release of circlator. For now, you could symlink python2 to point to python.

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commented Aug 9, 2016

Thanks a lot for all the kind helps! Now Circlator recognizes the spades version and works great on my mac!!

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