having problems with Trans-ABySS 1.5.3/python version

[Brian Novogradac]

Hello,

Hope someone has encountered this and can shed some light on how they got it working.  I am running Trans-ABySS 1.5.3 on a system with multiple versions of Python, i am having trouble getting it work work with the non default version (2.7.7)

I have edited the first line in my assemble script to #!/usr/local/bin/python2.7 

But t still failing with the following errror:

Trans-ABySS 1.5.3

CMD: /usr/local/bin/transabyss -k 25 --se ./reads/rnaseq_1.fq.gz ./reads/rnaseq_2.fq.gz --outdir ./test.k25 --name test.k25 --threads 2 --island 0 -c 1

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

Found Trans-ABySS directory at: /opt/transabyss

Found Trans-ABySS `bin` directory at: /opt/transabyss/bin

Found script at: /opt/transabyss/bin/skip_psl_self.awk

Found script at: /opt/transabyss/bin/skip_psl_self_ss.awk

Found `blat' at /usr/local/bin/blat

Found `MergeContigs' at /usr/local/bin/MergeContigs

Found `abyss-filtergraph' at /usr/local/bin/abyss-filtergraph

Found `abyss-map' at /usr/local/bin/abyss-map

Found `abyss-pe' at /usr/local/bin/abyss-pe

Found `abyss-junction' at /usr/local/bin/abyss-junction

# CPU(s) available: 96

# thread(s) requested: 2

# thread(s) to use: 2

CHECKPOINT: De Bruijn graph assembly was done previously. Will not re-run ...

Iteration 1 of graph simplification ...

ADJ: 76 vertices, 104 edges

Walked 3 paths and marked 12 vertices for removal.

CMD: bash -euo pipefail -c 'MergeContigs --kmer=25 --out=/scratch/XXX/XXX/XXX/DeNovo/TransABySS/Test/test.k25/test.k25-unitigs.r1.ref.fa /scratch/XXX/XXX/XXX/DeNovo/TransABySS/Test/test.k25/test.k25-1.fa /scratch/XXX/XXX/XXX/DeNovo/TransABySS/Test/test.k25/test.k25-1.adj /scratch/XXX/XXX/XXX/DeNovo/TransABySS/Test/test.k25/test.k25-unitigs.r1.ref.path'

The minimum coverage of single-end contigs is 1.

The minimum coverage of merged contigs is 1.

Traceback (most recent call last):

  File "/usr/local/bin/transabyss", line 748, in <module>

    __main__()

  File "/usr/local/bin/transabyss", line 531, in __main__

    unitig_assembly(fasta1, adj1, fasta3, adj3, tmp_file_prefix, island_size=args.island, max_iteration=args.iterations, k=args.k, strand_specific=args.stranded, min_percent_identity=args.p, seed_cov_grad=args.walk, indel_size_tolerance=args.indel, threads=args.threads, noblat=args.noblat)

  File "/usr/local/bin/transabyss", line 219, in unitig_assembly

    blat_self_align(ref_fasta1, ref_fasta1_selfalign_psl, percent_id=min_percent_identity, max_consecutive_edits=indel_size_tolerance, min_seq_len=k, threads=threads, skip_psl_self_awk=get_skip_psl_self_awk_script_path(strand_specific=strand_specific))

  File "/opt/transabyss/utilities/fasta_utils.py", line 50, in blat_self_align

    for a,b in itertools.combinations_with_replacement(files.keys(), 2):

AttributeError: 'module' object has no attribute 'combinations_with_replacement'

[Ka Ming Nip]

Hello Brian,

You would also need to set the environment variable `PYTHONPATH` if you haven't done so already.

Ka Ming

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Brian Novogradac [brian.no...@gmail.com]
Sent: May 30, 2016 7:37 AM
To: Trans-ABySS
Subject: having problems with Trans-ABySS 1.5.3/python version

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[Brian Novogradac]

I've already done that logged out and still same error

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[Ka Ming Nip]

How about calling python explicitly?

/usr/local/bin/python2.7 /usr/local/bin/transabyss -k 25 --se ...

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Brian Novogradac [brian.no...@gmail.com]

Sent: May 30, 2016 10:07 AM
To: Trans-ABySS
Subject: Re: having problems with Trans-ABySS 1.5.3/python version

I've already done that logged out and still same error

On Monday, May 30, 2016 at 12:21:33 PM UTC-4, Ka Ming Nip wrote:
Hello Brian,

You would also need to set the environment variable `PYTHONPATH` if you haven't done so already.

Ka Ming

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
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[Brian Novogradac]

It got past the initial error now i need to upgrade igraph to jgraph :(

Thanks Ka for the help

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[Ka Ming Nip]

Hi Brian,

Trans-ABySS doesn't use jgraph.

Instead of using the system-wide software, you can install all required software and modules (ie. python 2.7, pip, igraph, python-igraph, blat, samtools, EXCEPT FOR ABySS) under `transabyss/prereq` by running make:

cd transabyss/prereqs
make

It will take a while to install everything.
After that, update your `PATH` and `PYTHONPATH`:

export TRANSABYSS_PATH=transabyss/
export PATH=${TRANSABYSS_PATH}:${TRANSABYSS_PATH}/bin/:${TRANSABYSS_PATH}/prereqs/bin/:$PATH
export PYTHONPATH=${TRANSABYSS_PATH}

This method always works for me but not for everybody. You might want to give it a shot.
Hope that helps!

Ka Ming

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________

From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Brian Novogradac [brian.no...@gmail.com]

Sent: May 31, 2016 10:38 AM

To: Trans-ABySS
Subject: Re: having problems with Trans-ABySS 1.5.3/python version

It got past the initial error now i need to upgrade igraph to jgraph :(

Thanks Ka for the help


On Monday, May 30, 2016 at 1:20:26 PM UTC-4, Ka Ming Nip wrote:
How about calling python explicitly?

/usr/local/bin/python2.7 /usr/local/bin/transabyss -k 25 --se ...

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________

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[Brian Novogradac]

Is there anyway to only add certain this from that prereq make.  For example i do not want to install python 2.7, pip, igraph, python-igraph, blat, samtools i already have it installed system wide.  

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[Ka Ming Nip]

Yes, these are all the make targets for installing TransABySS:
bin
blat.COMPLETE
python.COMPLETE
python-igraph.COMPLETE

For example, this command will install `blat` and all of its dependencies according to the makefile:

make blat.COMPLETE

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Brian Novogradac [brian.no...@gmail.com]

Sent: June 1, 2016 5:54 AM

To: Trans-ABySS
Subject: Re: having problems with Trans-ABySS 1.5.3/python version

Is there anyway to only add certain this from that prereq make. For example i do not want to install python 2.7, pip, igraph, python-igraph, blat, samtools i already have it installed system wide.



On Tuesday, May 31, 2016 at 2:03:23 PM UTC-4, Ka Ming Nip wrote:
Hi Brian,

Trans-ABySS doesn't use jgraph.

Instead of using the system-wide software, you can install all required software and modules (ie. python 2.7, pip, igraph, python-igraph, blat, samtools, EXCEPT FOR ABySS) under `transabyss/prereq` by running make:

cd transabyss/prereqs
make

It will take a while to install everything.
After that, update your `PATH` and `PYTHONPATH`:

export TRANSABYSS_PATH=transabyss/
export PATH=${TRANSABYSS_PATH}:${TRANSABYSS_PATH}/bin/:${TRANSABYSS_PATH}/prereqs/bin/:$PATH
export PYTHONPATH=${TRANSABYSS_PATH}

This method always works for me but not for everybody. You might want to give it a shot.
Hope that helps!

Ka Ming

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________

To unsubscribe from this group and stop receiving emails from it, send an email to trans-abyss...@googlegroups.com<javascript:><mailto:trans-abyss...@googlegroups.com<javascript:><javascript:><javascript:>>.

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[Brian Novogradac]

I got it to finally work by installing python igraph separately.  

Thank s again for your help !!!