Spades version detection error

[uranus2001]

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]

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.

[uranus2001]

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]

Does

python2 spades.py

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

[uranus2001]

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.

[martinghunt]

Can you paste the output of

python2 `which spades.py`

[uranus2001]

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??

[martinghunt]

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]

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]

[martinghunt]

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.

[uranus2001]

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