Hello-

I'm trying to get transabyss set up on a server. I converted assemble.sh into a slurm script:

#!/bin/bash
cd /x/y/transabyss-master/sample_dataset/

ml python/2.7.14
export PYTHONPATH=$PYTHONPATH:/projects/[email protected]/python2.7/lib/python2.7/site-packages/

set -euo pipefail

cd $(dirname $0)

kmer1=25
kmer2=32
name1=test.k${kmer1}
name2=test.k${kmer2}
reads1=./reads/rnaseq_1.fq.gz
reads2=./reads/rnaseq_2.fq.gz
assemblydir1=./${name1}
assemblydir2=./${name2}
finalassembly1=${assemblydir1}/${name1}-final.fa
finalassembly2=${assemblydir2}/${name2}-final.fa
mergedassembly=./merged.fa

# set up the environment
TRANSABYSS_PATH=$(readlink -f ..)
export PATH=${TRANSABYSS_PATH}:${TRANSABYSS_PATH}/bin/:${PATH}

# assemble the test dataset
transabyss -k ${kmer1} --se ${reads1} ${reads2} --outdir ${assemblydir1} --name 
${name1} --threads 2 --island 0 -c 1

transabyss -k ${kmer2} --se ${reads1} ${reads2} --outdir ${assemblydir2} --name 
${name2} --threads 2 --island 0 -c 1

transabyss-merge --mink ${kmer1} --maxk ${kmer2} --prefixes k${kmer1}. k${kmer2}
. --out ${mergedassembly} ${finalassembly1} ${finalassembly2}

#EOF

The software seems to find all of the needed dependencies fine. However, now that I have that part figured out, I keep getting this error:

transabyss: error: No such file or directory ./reads/rnaseq_1.fq.gz

I have tried running the bash script from both transabyss-master and transabyss-master/sample_dataset with no luck. Do you know what my issue is?

Thanks,
Alissa Williams

Hello,

My RNA-seq data is strand-specific and is FR, and I find the trans-abyss (or abyss) option "--SS" expect the RF read (that is /1 read reverse, /2 read forward). Is there any existed method to handle it?
I've searched some forums like biostars, but no helpful results found.

At the moment, I only want to de novo assembly the RNA-Seq data. So what I care is whether use "--SS" to handle FR input data is proper for the assembly.

Hi! I'm encountering an issue with Trans-Abyss that appears to be a problem in the code. When executing the abyss-filtergraph command, it seems that too many arguments are being passed to the function abyss-filtergraph:

CMD: bash -euo pipefail -c 'abyss-filtergraph --shim --assemble --kmer=25 --island=0 --remove=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.braid.cids --graph=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.filtered.adj1 /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-1.adj /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-1.fa > /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.path'
abyss-filtergraph: too many arguments
Try abyss-filtergraph --help for more information.
ERROR: CMD ended with status code 1

I attempted to address this issue by removing the last argument, achieved by deleting this line, but the problem persists:

remove_rref_cmd_params1.append(last_good_fasta)

While attempting to merge the contigs, another issue arises:

CMD: bash -euo pipefail -c 'abyss-filtergraph --shim --assemble --kmer=25 --island=0 --remove=/home/apis/Gabriela_data_metagenomics/SRR1370499 2/25_assembly_trans_abyss-unitigs.r1.braid.cids --graph=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.f iltered.adj1 /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-1.adj > /home/apis/Gabriela_data_metagenomics/SRR137049 92/25_assembly_trans_abyss-unitigs.r1.path'
Elapsed time: 0 h 0 m 17 s
CMD: bash -euo pipefail -c 'MergeContigs --kmer=25 --out=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1. filtered.fa --adj --graph=/home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.filtered.adj /home/apis/Gabriel a_data_metagenomics/SRR13704992/25_assembly_trans_abyss-1.fa /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs .r1.filtered.adj1 /home/apis/Gabriela_data_metagenomics/SRR13704992/25_assembly_trans_abyss-unitigs.r1.path'
error: unexpected ID: 113'
Aborted (core dumped)
Elapsed time: 0 h 0 m 47 s
ERROR: CMD ended with status code 134

What should I do?

Hi Trans-abyss team,

I have a large dataset consisting of 99 libraries of ~35m reads each for a species that does not yet have a reference genome available and am interested in building a _de novo assembly. I have access to an HPC cluster (24 core, 250 Gb RAM) and have setup trans-abyss with singularity.

I am unsure whether it would be better to assemble a single transcriptome using all libraries or assemble each library separately and then merge them.

Based on your experience with your assembler, can you make any strategy recommendations based on my available computing resources?

@sjackman @kmnip Hello! Could you please update conda version to 2.01?

Hi folks,

I attempted to assemble fungal transcriptome using PE and SE reads of which I performed reverse-complement using BBMap reformat.sh. However, I ran into several issues:

1. The assembler was unable to detect my read orientation which I identified as inwards, stranded and forward (ISF) using Salmon. The assembler declared the library as FF after detecting 112 reads while declared most of the reads as different (I don't know the definition of Different here)

2. The assemble stopped with status code 2

I attached the screenshot for your reference. Is there any solution that I can try? Thank you in advance!

Howdy Trans-ABySS,

I downloaded the latest Trans-ABySS upload to bioconda (noarch/transabyss-2.0.1-py_6.tar.bz2) on Ubuntu 20.04 and when downloading the ICU dependency, it downloads v67.1:

Collecting package metadata (repodata.json): done
Solving environment: done

Package Plan

  environment location: /home/alexanderselvey/miniconda3/envs/transabyss

  added / updated specs:
    - transabyss


The following NEW packages will be INSTALLED:

  abyss              bioconda/linux-64::abyss-2.0.2-h51208dd_5
  blat               bioconda/linux-64::blat-36-0
  bwa                bioconda/linux-64::bwa-0.7.17-hed695b0_7
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h516909a_2
  cairo              conda-forge/linux-64::cairo-1.16.0-h3fc0475_1004
  curl               conda-forge/linux-64::curl-7.69.1-h33f0ec9_0
  fontconfig         conda-forge/linux-64::fontconfig-2.13.1-h1056068_1002
  freetype           conda-forge/linux-64::freetype-2.10.2-he06d7ca_0
  gettext            conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002
  glib               conda-forge/linux-64::glib-2.64.3-h6f030ca_0
  gmp                conda-forge/linux-64::gmp-6.2.0-he1b5a44_2
  icu                conda-forge/linux-64::icu-67.1-he1b5a44_0
  igraph             conda-forge/linux-64::igraph-0.7.1-4
  krb5               conda-forge/linux-64::krb5-1.17.1-h2fd8d38_0
  libcurl            conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0
  libdeflate         bioconda/linux-64::libdeflate-1.0-h14c3975_1
  libedit            conda-forge/linux-64::libedit-3.1.20191231-h46ee950_0
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_6
  libiconv           conda-forge/linux-64::libiconv-1.15-h516909a_1006
  libpng             conda-forge/linux-64::libpng-1.6.37-hed695b0_1
  libssh2            conda-forge/linux-64::libssh2-1.9.0-hab1572f_2
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
  libxcb             conda-forge/linux-64::libxcb-1.13-h14c3975_1002
  libxml2            conda-forge/linux-64::libxml2-2.9.10-h72b56ed_1
  make               conda-forge/linux-64::make-4.3-h516909a_0
  mpi                conda-forge/linux-64::mpi-1.0-openmpi
  openmpi            conda-forge/linux-64::openmpi-4.0.3-hdf1f1ad_1
  pandoc             conda-forge/linux-64::pandoc-2.9.2.1-0
  pcre               conda-forge/linux-64::pcre-8.44-he1b5a44_0
  perl               conda-forge/linux-64::perl-5.26.2-h516909a_1006
  pixman             conda-forge/linux-64::pixman-0.38.0-h516909a_1003
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
  pycairo            conda-forge/linux-64::pycairo-1.19.1-py38h323dad1_3
  python-igraph      conda-forge/linux-64::python-igraph-0.7.1.post7-py38h516909a_0
  samtools           bioconda/linux-64::samtools-1.9-h8571acd_11
  transabyss         bioconda/noarch::transabyss-2.0.1-py_6
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002
  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007

When I run $transabyss I get this error:

Traceback (most recent call last):
  File "/home/alexanderselvey/miniconda3/envs/transabyss/bin/transabyss", line 18, in <module>
    from transabyss.adj_utils import has_edges
  File "/home/alexanderselvey/miniconda3/envs/transabyss/lib/python3.8/site-packages/transabyss/adj_utils.py", line 6, in <module>
    import igraph
  File "/home/alexanderselvey/miniconda3/envs/transabyss/lib/python3.8/site-packages/igraph/__init__.py", line 34, in <module>
    from igraph._igraph import *
ImportError: libicui18n.so.58: cannot open shared object file: No such file or directory

I remedied that by downloading ICU v58.2 with conda install icu=58.*

It now works. I'm not sure if you can set the particular ICU dependency it downloads with, but if so, it should be set to ICU v58.2 to prevent others from running into this issue.

Thanks!

good morning

I installed Trans ABySS with conda, but for some reason the awk scripts are not being found. Where do I need to put them so they're found?
When I enter
$ transabyss

I get the following message:
"
Trans-ABySS 1.5.4
CMD: /data/software/Python/anaconda2/bin/transabyss
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Found Trans-ABySS directory at: /data/software/Python/anaconda2/lib/python2.7/site-packages
Found Trans-ABySS bin directory at: /data/software/Python/anaconda2/lib/python2.7/site-packages/bin
No such file: skip_psl_self.awk
No such file: skip_psl_self_ss.awk
Found blat' at /data/software/Python/anaconda2/bin/blat Found MergeContigs' at /data/software/abyss-2.0.2/MergePaths/MergeContigs
Found abyss-filtergraph' at /data/software/abyss-2.0.2/FilterGraph/abyss-filtergraph Found abyss-map' at /data/software/abyss-2.0.2/Map/abyss-map
Found abyss-pe' at /data/software/abyss-2.0.2/bin/abyss-pe Found abyss-junction' at /data/software/abyss-2.0.2/Scaffold/abyss-junction
ERROR: Your environment is not sufficient to run Trans-ABySS. Please check the missing executables, scripts, or directories.
"
Where would I expect these files to be?

Kind regards,

Anne

I need to work with transabyss for RNAseq analysis, I am unable to install abyss1.5.2 as the make fails for one or other module (Layout, Overlap,Konnector,etc) depending on what boost I use. I have tried the latest boost (1.64.0) as well several other (1.55.0,1.52.0,1.40.0) to configure and make abyss but I have failed. I even tried installing transabyss 1.5.3 with abyss 1.5.1 but failed to do so too. Could you please help me with this. I am working on Fedora 4.8

1. how to install abyss1,5,2 successfully for using transabyss? Which boost library to use?
   2.Can I use the latest abyss2.0 for transabyss 1.5.5?

Thanks

Hi,

I want to run transabyss v 2.0.1 without mpi but I do not seem to be able to do so. Even when I add the option --mpi 0 it still starts the ABYSS-P with mpi .

is there perhaps some other tick to get the desired behaviour? I do want to run it multi-threaded but not mpi.

thx

From the github page it appears as if any python above 2.7.10 is supported. Does that include python 3? If so, then I have a bug to report:

python3 ~/down/transabyss-2.0.0/transabyss
Traceback (most recent call last):
  File "/Users/winni/down/transabyss-2.0.0/transabyss", line 17, in <module>
    from utilities import psl_cid_extractor
  File "/Volumes/mac-3/home/Downloads/transabyss-2.0.0/utilities/psl_cid_extractor.py", line 140
    print cid
            ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(print cid)?

Hi
We are trying to run a de novo assembly on a local server.
Trans-ABySS 2.0.1
CMD: /home/[email protected]/src/transabyss-2.0.1/transabyss -k 35 --pe /home/[email protected]/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz /home/[email protected]/gregarine/transabyss_assemblies/reads/E8R2AT2_2.clean.fq.gz --outdir /home/[email protected]/gregarine/transabyss_assemblies --name k35.transabyss.fa --threads 20 -c 12

It appears to initialize OK:
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Found Trans-ABySS directory at: /home/[email protected]/src/transabyss-2.0.1
Found Trans-ABySS bin directory at: /home/[email protected]/src/transabyss-2.0.1/bin
Found script at: /home/[email protected]/src/transabyss-2.0.1/bin/skip_psl_self.awk
Found script at: /home/[email protected]/src/transabyss-2.0.1/bin/skip_psl_self_ss.awk
Found abyss-pe' at /home/[email protected]/miniconda3/bin/abyss-pe Found MergeContigs' at /home/[email protected]/miniconda3/bin/MergeContigs
Found abyss-filtergraph' at /home/[email protected]/miniconda3/bin/abyss-filtergraph Found abyss-junction' at /home/[email protected]/miniconda3/bin/abyss-junction
Found blat' at /usr/local/bin/blat Found abyss-map' at /home/[email protected]/miniconda3/bin/abyss-map

CPU(s) available: 24

thread(s) requested: 20

thread(s) to use: 20

CMD: bash -euo pipefail -c 'abyss-pe graph=adj --directory=/home/[email protected]/gregarine/transabyss_assemblies k=35 name=k35.transabyss.fa E=0 e=12 c=12 j=20 k35.transabyss.fa-1.fa k35.transabyss.fa-1.adj q=3 se="/home/[email protected]/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz /home/[email protected]/gregarine/transabyss_assemblies/reads/E8R2AT2_2.clean.fq.gz"'

but then this error appears:
make: Entering directory '/home/[email protected]/gregarine/transabyss_assemblies'
which: no abyss-pe.Makefile in (/home/[email protected]/miniconda3/bin)
dirname: missing operand
Try 'dirname --help' for more information.

after which it appears to continue to run but is taking along time to read in the reads.:
ABYSS -k35 -q3 -e12 -E0 -c12 --coverage-hist=coverage.hist -s k35.transabyss.fa-bubbles.fa -o k35.transabyss.fa-1.fa /home/[email protected]/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz /home/[email protected]/gregarine/transabyss_assemblies/reads/E8R2AT2_2.clean.fq.gz
ABySS 2.0.2
ABYSS -k35 -q3 -e12 -E0 -c12 --coverage-hist=coverage.hist -s k35.transabyss.fa-bubbles.fa -o k35.transabyss.fa-1.fa /home/[email protected]/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz /home/[email protected]/gregarine/transabyss_assemblies/reads/E8R2AT2_2.clean.fq.gz
Reading `/home/[email protected]/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz'...

looking at processes running on the server, both ABYSS & gzip are running.

Just wondering about the 'no abyss-pe.Makefile ' msg?
Charles

Although the paired reads were checked with two different scripts for unpaired reads before running TransAbyss-Analyze, an error saying "the paired-end accessions do not match" is output before aborting. The message essentially says Paired-end accessions FCC6B7TACXX:7:1101:10524:57301# and FCC6B7TACXX:7:1101:9245:1994# do not match.

Command:

transabyss-analyze -a TrAb_Merged_1_1.fa -1 RG11_NR_P3_R1.fq.gz -2 RG11_NR_P3_R2.fq.gz --SS --ref Gh1 --cfg /work/satishg/transcriptome.cfg --annodir /work/satishg/Gh1.gtf --analyze fusion -o /work/satishg/TrAn_RG11_Gh1 -t 20

Error Message:

/work/satishg/TrAn_RG11_Gh1/reads_to_genome/cluster/transabyss.local.sh: line 3: ulimit: core file size: cannot modify limit: Operation not permitted
GSNAP version 2014-12-29 called with args: gsnap --gunzip -d Gh1 -D /work/satishg -t 18 --format sam -N 1 -m 10 /work/satishg/RG11_NR_P3_R1.fq.gz /work/satishg/RG11_NR_P3_R2.fq.gz
Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17 
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=-58 => compiler sign extends
Finished checking compiler assumptions
Novel splicing (-N) turned on => assume reads are RNA-Seq
Paired-end accessions FCC6B7TACXX:7:1101:10524:57301# and FCC6B7TACXX:7:1101:9245:1994# do not match
real    0m0.623s
user    0m0.009s
sys     0m0.056s
ERROR: Execution of script ended with a non-zero exit-status.

I tried running it with three different read pairs but all terminate with the same error.
Please suggest a fix for the same.

Hi, I'm trying to install Trans-Abyss through Conda, but apparently it's not longer available,
There's another way to install it?

(Miscpy27) [larteag7@cronos Purpureocillium]$ conda install -c bioconda transabyss
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - transabyss
  - python-igraph

Current channels:

  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/linux-64
  - https://repo.anaconda.com/pkgs/pro/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Thanks in advance,
Luis Alfonso.

This is just a question to make sure I understood the README.md correctly. If I want to assemble regular paired-end reads stored in separate files (not strand-specific), then the correct way to do that is with this command?

transabyss --se forward.fq.gz reverse.fq.gz --pe forward.fq.gz reverse.fq.gz

We are getting later run-errors with ABYSS 2.0.2 in conjunction with Trans-ABySS, which is basically a known issue. bcgsc/abyss#159

reads containing non-ACGT characters make: *** No rule to make target 'transabyss-1.adj'. Stop.

If there is anything to instrument this on the pipelines used for debugging, would be happy to help.

Hi,
I'm implementing Trans-ABySS in an SLURM HPC system,
when I call the CMD in the master node the script calls abyss-pe, but for some reason when I call the CMD in some other node is calling ABYSS-P instead of abyss-pe,
I tried suppresing the MPI processes in the CMD with mpi 0 but it's not working (as you can see the following out)

Trans-ABySS 2.0.1
CMD: /home/larteag7/apps/transabyss-2.0.1/transabyss --se sym-single.fq sym-interleaved.fq --pe sym-interleaved.fq --outdir /home/larteag7/my-thesis/frl-2015/transabyss-default --name transabyss-dft --threads 16 --mpi 0
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Found Trans-ABySS directory at: /home/larteag7/apps/transabyss-2.0.1
Found Trans-ABySS `bin` directory at: /home/larteag7/apps/transabyss-2.0.1/bin
Found script at: /home/larteag7/apps/transabyss-2.0.1/bin/skip_psl_self.awk
Found script at: /home/larteag7/apps/transabyss-2.0.1/bin/skip_psl_self_ss.awk
Found `abyss-pe' at /home/larteag7/.conda/envs/abyss/bin/abyss-pe
Found `MergeContigs' at /home/larteag7/.conda/envs/abyss/bin/MergeContigs
Found `abyss-filtergraph' at /home/larteag7/.conda/envs/abyss/bin/abyss-filtergraph
Found `abyss-junction' at /home/larteag7/.conda/envs/abyss/bin/abyss-junction
Found `blat' at /home/larteag7/.conda/envs/abyss/bin/blat
Found `abyss-map' at /home/larteag7/.conda/envs/abyss/bin/abyss-map
# CPU(s) available:     16
# thread(s) requested:  16
# thread(s) to use:     16
CMD: bash -euo pipefail -c 'abyss-pe graph=adj --directory=/home/larteag7/my-thesis/frl-2015/transabyss-default k=32 name=transabyss-dft E=0 e=2 c=2 j=16 transabyss-dft-1.fa transabyss-dft-1.adj q=3 se="/home/larteag7/my-thesis/frl-2015/sym-interleaved.fq /home/larteag7/my-thesis/frl-2015/sym-single.fq /home/larteag7/my-thesis/frl-2015/sym-interleaved.fq"'
make: Entering directory `/home/larteag7/my-thesis/frl-2015/transabyss-default'
mpirun -np 16 ABYSS-P -k32 -q3 -e2 -E0 -c2    --coverage-hist=coverage.hist -s transabyss-dft-bubbles.fa  -o transabyss-dft-1.fa  /home/larteag7/my-thesis/frl-2015/sym-interleaved.fq /home/larteag7/my-thesis/frl-2015/sym-single.fq /home/larteag7/my-thesis/frl-2015/sym-interleaved.fq
make: Leaving directory `/home/larteag7/my-thesis/frl-2015/transabyss-default'
ERROR: CMD ended with status code 2

Is something wrong with the CMD or the installation,
Thanks in advance,
Luis Alfonso.

Hi,
Just reporting an issue with Python3,

Traceback (most recent call last):
  File "/home/bio/anaconda3/bin/transabyss", line 4, in <module>
    __import__('pkg_resources').run_script('transabyss==1.54', 'transabyss')
  File "/home/bio/anaconda3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 658, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/bio/anaconda3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1438, in run_script
    exec(code, namespace, namespace)
  File "/home/bio/anaconda3/lib/python3.6/site-packages/transabyss-1.54-py3.6.egg-info/scripts/transabyss", line 19, in <module>
    from transabyss.adj_utils import has_edges
  File "/home/bio/anaconda3/lib/python3.6/site-packages/transabyss/adj_utils.py", line 7, in <module>
    import igraph
  File "/home/bio/anaconda3/lib/python3.6/site-packages/igraph/__init__.py", line 8, in <module>
    raise DeprecationWarning("To avoid name collision with the igraph project, "
DeprecationWarning: To avoid name collision with the igraph project, this visualization library has been renamed to 'jgraph'. Please upgrade when convenient.

Cheers!
Luis Alfonso.

Do you recommend to trim polyA tails from the raw data when assembling transcriptomes using Trans-ABySS?

Hi,

I tried transabyss (k32) on my university cluster on 40gb RNASeq data, following your short tutorial, and it is stuck because it used all 384gb of the node and also swaped! I think it is really strange to require so much memory! Do you have any thoughts?

Hi,
I installed transabyss via bioconda, within the Oyster River Protocol, after working a first time, now i get a missing files error:

Found Trans-ABySS directory at: 
/mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/lib/python3.6/site-packages
Found Trans-ABySS `bin` directory at: /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/lib/python3.6/site-packages/bin
No such file: skip_psl_self.awk
No such file: skip_psl_self_ss.awk
Found `abyss-pe' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/abyss-pe
Found `MergeContigs' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/MergeContigs
Found `abyss-filtergraph' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/abyss-filtergraph
Found `abyss-junction' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/abyss-junction
Found `blat' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/blat
Found `abyss-map' at /mnt/DATA/Software/Oyster_River_Protocol/software/anaconda/install/envs/orp/bin/abyss-map
ERROR: Your environment is not sufficient to run Trans-ABySS. Please check the missing executables, scripts, or directories.

do you have any insight?
Thanks

EDIT:
there was a conflicting version installed, re-exporting path fixed the essue

I got the following error msg by running:
bash sample_dataset/assemble.sh

I just installed and tried to run the sample assembly, however, blat 35 fails with an internal error:

$ bash sample_dataset/assemble.sh
...
CHECKPOINT: De Bruijn graph assembly completed.
Iteration 1 of graph simplification ...
ADJ: 42 vertices, 48 edges
Walked 3 paths and marked 8 vertices for removal.
CMD: bash -euo pipefail -c 'MergeContigs --kmer=32 --out=/tmp/transabyss-1.5.2/sample_dataset/test/assembly/test-unitigs.r1.ref.fa /tmp/transabyss-1.5.2/sample_dataset/test/assembly/test-1.fa /tmp/transabyss-1.5.2/sample_dataset/test/assembly/test-1.adj /tmp/transabyss-1.5.2/sample_dataset/test/assembly/test-unitigs.r1.ref.path'
The minimum coverage of single-end contigs is 1.
The minimum coverage of merged contigs is 1.
Internal error genoFind.c 2250Internal error genoFind.c 2250

CMD: bash -euo pipefail -c 'blat -noHead -t=dna -q=dna -out=psl -tileSize=18 -maxGap=1 -maxIntron=1 -minScore=638 /tmp/transabyss-1.5.2/sample_dataset/test/assembly/test-unitigs.r1.ref.fa.1 /tmp/transabyss-1.5.2/sample_dataset/test/assembly/test-unitigs.r1.ref.fa.1 >(/tmp/transabyss-1.5.2/bin/skip_psl_self.awk > /tmp/transabyss-1.5.2/sample_dataset/test/assembly/test-unitigs.r1.ref.fa.selfalign.psl.0) >&2'
ERROR: CMD ended with status code 255
Internal error genoFind.c 2250Internal error genoFind.c 2250

Hello there,

I am using Trans-ABySS to assemble a transcriptome for my pair-end RNAseq data (3 replicates x 50 genotypes). I installed Trans-ABySS (v2.0.1) through conda on a Linux server. The commands are following
file_list=($(find /liyong_temp/trimmed/ -type f -name "*P.fq.gz" | sort))
out=/transcriptome_assembly/de_novo/transabyss
transabyss \ --pe ${file_list[@]} \ --threads 64 \ --length 200 \ --outdir $out

The log file is:
/liyong_temp/trimmed/Cs123_trimmed_1P.fq.gz': discarded 5 reads containing non-ACGT characters
/liyong_temp/trimmed/Cs123_trimmed_2P.fq.gz': discarded 62 reads containing non-ACGT characters
........................
/liyong_temp/trimmed/Cs133_trimmed_1P.fq.gz': discarded 2 reads containing non-ACGT characters
/liyong_temp/trimmed/Cs133_trimmed_2P.fq.gz': discarded 16 reads containing non-ACGT characters

The minimum coverage of single-end contigs is 2.
The minimum coverage of merged contigs is 2.
The minimum coverage of single-end contigs is 0.652174.
The minimum coverage of merged contigs is 2.
Consider increasing the coverage threshold parameter, c, to 2.
The minimum coverage of single-end contigs is 2.
The minimum coverage of merged contigs is 2.
warning: the seed-length should be at least twice k: k=32, s=32
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
sort: write failed: /tmp/sortUz7aTQ: No space left on device
error: `transabyss-3.hist': No such file or directory
make: *** [/home/AGR.GC.CA/zhangliy/transabyss_conda/env/bin/abyss-pe.Makefile:559: transabyss-3.dist] Error 1
make: *** Deleting file 'transabyss-3.dist'

Any suggestion how I could get this to work?
Many thanks.

Hi everyone,
Running trans-abyss, the process is aborted and I'm stuck in this error:

/share/apps/openmpi/1.10.7/gcc/5.4.0/bin/mpirun: error while loading shared libraries: libslurm.so.30: cannot open shared object file: No such file or directory
make: *** [transabyss-dft-1.fa] Error 127

This is the program out:

Trans-ABySS 2.0.1
CMD: /home/larteag7/apps/transabyss-2.0.1/transabyss --se sym-single.fq sym-interleaved.fq --pe sym-interleaved.fq --outdir /home/larteag7/my-thesis/frl-2015/transabyss-default --name transabyss-dft --cleanup 2
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Found Trans-ABySS directory at: /home/larteag7/apps/transabyss-2.0.1
Found Trans-ABySS `bin` directory at: /home/larteag7/apps/transabyss-2.0.1/bin
Found script at: /home/larteag7/apps/transabyss-2.0.1/bin/skip_psl_self.awk
Found script at: /home/larteag7/apps/transabyss-2.0.1/bin/skip_psl_self_ss.awk
Found `abyss-pe' at /home/larteag7/.conda/envs/abyss/bin/abyss-pe
Found `MergeContigs' at /home/larteag7/.conda/envs/abyss/bin/MergeContigs
Found `abyss-filtergraph' at /home/larteag7/.conda/envs/abyss/bin/abyss-filtergraph
Found `abyss-junction' at /home/larteag7/.conda/envs/abyss/bin/abyss-junction
Found `blat' at /home/larteag7/.conda/envs/abyss/bin/blat
Found `abyss-map' at /home/larteag7/.conda/envs/abyss/bin/abyss-map
# CPU(s) available:     32
# thread(s) requested:  1
# thread(s) to use:     1
Creating output directory: /home/larteag7/my-thesis/frl-2015/transabyss-default
CMD: bash -euo pipefail -c 'abyss-pe graph=adj --directory=/home/larteag7/my-thesis/frl-2015/transabyss-default k=32 name=transabyss-dft E=0 e=2 c=2 j=1 transabyss-dft-1.fa transabyss-dft-1.adj q=3 se="/home/larteag7/my-thesis/frl-2015/sym-interleaved.fq /home/larteag7/my-thesis/frl-2015/sym-single.fq /home/larteag7/my-thesis/frl-2015/sym-interleaved.fq"'
make: Entering directory `/home/larteag7/my-thesis/frl-2015/transabyss-default'
/share/apps/openmpi/1.10.7/gcc/5.4.0/bin/mpirun -np 16 ABYSS-P -k32 -q3 -e2 -E0 -c2    --coverage-hist=coverage.hist -s transabyss-dft-bubbles.fa  -o transabyss-dft-1.fa  /home/larteag7/my-thesis/frl-2015/sym-interleaved.fq /home/larteag7/my-thesis/frl-2015/sym-single.fq /home/larteag7/my-thesis/frl-2015/sym-interleaved.fq
make: Leaving directory `/home/larteag7/my-thesis/frl-2015/transabyss-default'
ERROR: CMD ended with status code 2

This is the information of abyss-pe and my OS:

(abyss) [larteag7@apolo frl-2015]$ abyss-pe --version
GNU Make 3.81
Copyright (C) 2006  Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

This program built for x86_64-redhat-linux-gnu
(abyss) [larteag7@apolo frl-2015]$ lsb_release -d
Description:	CentOS release 6.6 (Final)

These are the versions of openmpi available:

openmpi-1.10-x86_64                       openmpi/1.8.8-x86_64_gcc-5.4.0_cuda-7.0
openmpi/1.8.8_gcc-5.4.0                   openmpi/1.8.8-x86_64_gcc-5.4.0_cuda-8.0
openmpi/1.8.8_gcc-5.4.0_cuda-8.0          openmpi/1.8.8-x86_64_intel-2017_update-1
openmpi/1.8.8_no-pmi_intel-2017_update-1  openmpi-1.8-x86_64
openmpi/1.8.8-x86_64_gcc-5.4.0            openmpi-x86_64

I've tried loading slurm libraries, different versions of openmpi, and so on,
What's happening and how can I fix it?

Cheers,
Luis Alfonso.

Hi,

I'm running transabyss v 2.0.1 with default settings.
When checking the run-logs I was a little surprised to see the following message:
warning: the seed-length should be at least twice k: k=32, s=32
and indeed the default for s is set to k it says in the manual/help .
Would it therefore not be better to set the default for s to k*2 by default?

thx.

Hi,

I can't seem to get the sample_dataset to assemble. I keep hitting an assert early into the assembly process:

./sample_dataset/assemble.sh
Trans-ABySS 1.5.4
CMD: /src/transabyss/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: /src/transabyss
Found Trans-ABySS `bin` directory at: /src/transabyss/bin
Found script at: /src/transabyss/bin/skip_psl_self.awk
Found script at: /src/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: 8
# thread(s) requested:  2
# thread(s) to use: 2
CMD: bash -euo pipefail -c 'abyss-pe --directory=/src/transabyss/sample_dataset/test.k25 k=25 name=test.k25 E=0 e=1 c=1 j=2 test.k25-1.fa test.k25-1.adj q=3 se="/src/transabyss/sample_dataset/reads/rnaseq_1.fq.gz /src/transabyss/sample_dataset/reads/rnaseq_2.fq.gz"'
make: Entering directory `/src/transabyss/sample_dataset/test.k25'
make: `test.k25-1.fa' is up to date.
AdjList    -k25 -m50 --adj test.k25-1.fa >test.k25-1.adj
make: Leaving directory `/src/transabyss/sample_dataset/test.k25'
CHECKPOINT: De Bruijn graph assembly completed.
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=/src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.ref.fa /src/transabyss/sample_dataset/test.k25/test.k25-1.fa /src/transabyss/sample_dataset/test.k25/test.k25-1.adj /src/transabyss/sample_dataset/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.
Loaded 392 letters in 8 sequences
Loaded 1700 letters in 1 sequences
Searched 392 bases in 8 sequences
Searched 392 bases in 8 sequences
Loaded 701 letters in 1 sequences
Loaded 1166 letters in 1 sequences
Searched 392 bases in 8 sequences
Searched 392 bases in 8 sequences
Loaded 1700 letters in 1 sequences
Loaded 1700 letters in 1 sequences
Searched 701 bases in 1 sequences
Searched 1700 bases in 1 sequences
Loaded 701 letters in 1 sequences
Loaded 1700 letters in 1 sequences
Searched 1166 bases in 1 sequences
Searched 701 bases in 1 sequences
Loaded 1166 letters in 1 sequences
Loaded 1166 letters in 1 sequences
Searched 701 bases in 1 sequences
Searched 1166 bases in 1 sequences
8 potentially removable paths ...
Marked 16 more vertices for removal.
CMD: bash -euo pipefail -c 'abyss-filtergraph --shim --kmer=25 --island=0 --remove=/src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.rm.cids --graph=/src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.filtered.adj1 /src/transabyss/sample_dataset/test.k25/test.k25-1.adj > /src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.path1'
CMD: bash -euo pipefail -c 'abyss-filtergraph --no-shim --assemble --kmer=25 --island=0 --graph=/src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.filtered.adj /src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.filtered.adj1 > /src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.path'
CMD: bash -euo pipefail -c 'MergeContigs --kmer=25 --out=/src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.filtered.fa /src/transabyss/sample_dataset/test.k25/test.k25-1.fa /src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.filtered.adj1 /src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.path'
The minimum coverage of single-end contigs is 210.747.
The minimum coverage of merged contigs is 210.747.
Completed iteration 1 of graph simplification.
Iteration 2 of graph simplification ...
ADJ: 32 vertices, 26 edges
Walked 3 paths and marked 0 vertices for removal.
CMD: bash -euo pipefail -c 'MergeContigs --kmer=25 --out=/src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r2.ref.fa /src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.filtered.fa /src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r1.filtered.adj /src/transabyss/sample_dataset/test.k25/test.k25-unitigs.r2.ref.path'
MergeContigs: MergeContigs.cpp:547: int main(int, char**): Assertion `!contigs.empty()' failed.
Aborted (core dumped)
ERROR: CMD ended with status code 134

Any ideas or suggestions?