idba segmentation fault

bernt-matthias commented 3 years ago

Dear rnaQUAST developers,

I got the following error logs from rnaquast:

https://gist.github.com/bernt-matthias/2f6f39beea442aad7f9141093f8a44bb

Do you have any advice how I could find out what is going wrong?

martsper commented 3 years ago

Hi,

I think I encountered the same problem. I got the following error with: python rnaQUAST.py --test

2021-04-08 17:51:38 Aligning idba to Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.upper... log can be found in /home/martin/anaconda3/bin/rnaQUAST_test_output/logs/gmap.idba.err.log. ERROR! gmap failed for idba! gmap.idba.err.log

I attached the log file. (I am new to rnaQUAST, I tried to install it today for the first time)

Best, Martin

bernt-matthias commented 3 years ago

Are you also running on a conda installation?

bernt-matthias commented 3 years ago

Strange thing is that the test returns exit code 0 .. but this might be fixed here https://github.com/ablab/rnaquast/pull/8

bernt-matthias commented 3 years ago

Seem to work with gmap 2020.10.14 .. but fails with 2021-02-22 (these are the last versions of gmap in bioconda).

martsper commented 3 years ago

Hi, I set up a brand new ubunut (20.04 LTS) with the latest miniconda3, created a fresh environment and tried to install rnaQUAST with "conda install -c bioconda rnaquast". However, the installation hangs at the solving environment step. Then, I tried again with anaconda3 and a fresh environment, under which at least I could install rnaQUAST with "conda install -c bioconda rnaquast". However, running "python rnaQUAST.py --test" resulted in the same error as mentioned above. What would be a correct way to downgrade gmap within a conda environment?

bernt-matthias commented 3 years ago

Actually in the most recent rnaquast recipe (merged a few hours ago) I restricted gmap to <2021.02.22.

Can you check with conda list | egrep "gmap|quast" which builds are installed? For me it is:

gmap                      2020.10.14      pl526h2f06484_0    bioconda
rnaquast                  2.2.0                h9ee0642_2    https://149550-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages

if needed, you may downgrade gmap with conda install -c bioconda -c conda-forge "gmap<2021.02.22".

martsper commented 3 years ago

Hi, this is what was just installed with "conda install -c bioconda rnaquast"

gmap                      2021.02.22      pl526h2f06484_0    bioconda
rnaquast                  2.0.1                         0    bioconda

Thanks for the tip with the downgrade, I will try

martsper commented 3 years ago

I downgraded gmap as you suggested. This worked fine. Basically, I have now an environment with the following builds:

gmap                      2020.10.14      pl526h2f06484_0    bioconda
rnaquast                  2.0.1                         0    bioconda

Here is the log: rnaQUAST.log

Now its only strange why "conda install -c bioconda rnaquast" resulted in gmap 2021.02.22 and rnaQUAST 2.0.1

bernt-matthias commented 3 years ago

Actually the odd thing is that you get rnaquast 2.0.1 and not 2.2.0.

The new restriction for the gmap version only happens for 2.2.0 (build 2 or greater).

mmcardozo commented 3 years ago

Dear rnaquast team,

I'm also experiencing a similar problem when running: rnaQUAST.py --test

2021-04-12 10:08:15,136 - INFO - Committing changes: 42000 features 2021-04-12 10:08:15,370 - INFO - Populating features table and first-order relations: 42246 features 2021-04-12 10:08:15,373 - INFO - Creating relations(parent) index 2021-04-12 10:08:15,399 - INFO - Creating relations(child) index 2021-04-12 10:08:15,430 - INFO - Creating features(featuretype) index 2021-04-12 10:08:15,444 - INFO - Creating features (seqid, start, end) index 2021-04-12 10:08:15,458 - INFO - Creating features (seqid, start, end, strand) index 2021-04-12 10:08:15,473 - INFO - Running ANALYZE features ERROR! gmap failed for idba!

Here is the log file for rnaquast rnaQUAST.log

Many thanks, Magda

martsper commented 3 years ago

Hi,

on my end, rnaquast is now running smoothly, having the following versions installed:

gmap                      2020.10.14      pl526h2f06484_0    bioconda
rnaquast                  2.2.0                h9ee0642_2    bioconda

@mmcardozo: In your log file it says that you have an "unkown" gmap version, which appears odd. You could try to update your rnaquast package, or install/update gmap to version 2020.10.14 as described by Matthias.

A stupid workaround would be to run rnaquast with the "--blat" flag (then it uses BLAT, instead of GMAP).

Best, Martin

mmcardozo commented 3 years ago

Hi,

Thank you for your suggestions! I installed gmap the older version as you suggested 2020.10.14:

conda create --strict-channel-priority -c conda-forge -c bioconda -c defaults -n rnaquast rnaquast matplotlib joblib gffutils busco blast hmmer blat idba "gmap<2021.02.22"

However the error is the same...

/home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/share/rnaquast-2.2.0-2/rnaQUAST.py --transcripts /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/share/rnaqua

rnaQUAST: 2.2.0

System information: OS: Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-glibc2.17 (linux_64) Python version: 3.9.2 CPUs number: 36

External tools: matplotlib: 3.4.1 joblib: 1.0.1 gffutils: 0.10.1 blastn: 2.11.0+ makeblastdb: 2.11.0+ gmap: unknown

Started: 2021-04-12 19:57:36

Logging to /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/rnaQUAST.log

NOTICE: Maximum number of threads is set to 16 (use --threads option to set it manually)

2021-04-12 19:57:36 Getting reference... Done. Using non strand specific transcripts...

2021-04-12 19:57:36 Creating sqlite3 db by gffutils... saved to /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/rnaQUAST_test_output/Saccharomyces_cerevisiae.R64-1-1.75.db.

2021-04-12 19:57:41 Loading sqlite3 db by gffutils from /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/rnaQUAST_test_output/Saccharomyces_cerevisiae.R64-1-1.75.db to memory... Done.

2021-04-12 19:57:42 Getting GENE DATABASE metrics... Done.

Sets maximum intron size equal 2583. Default is 1500000 bp.

2021-04-12 19:57:49 Sorting exons attributes... Sorted in I. Sorted in II. Sorted in III. Sorted in IV. Sorted in IX. Sorted in Mito. Sorted in V. Sorted in VI. Sorted in VII. Sorted in VIII. Sorted in X. Sorted in XI. Sorted in XII. Sorted in XIII. Sorted in XIV. Sorted in XV. Sorted in XVI. Done.

2021-04-12 19:57:50 Getting transcripts from /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/idba.fasta... Done.

2021-04-12 19:57:50 Getting transcripts from /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/Trinity.fasta... Done.

2021-04-12 19:57:50 Getting transcripts from /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/spades.311.fasta... Done.

2021-04-12 19:57:50 Getting upper case fasta... saved to /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.upper.fa

2021-04-12 19:57:50 Creating genome index by gmap_build... logs can be found in /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/gmap_build.out.log and /home/ollie/mcardozo/ownSoft/miniconda3 saved to /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.upper

GMAP_BUILD TIME: 0:00:30.962474

2021-04-12 19:58:21 Aligning idba to Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.upper... log can be found in /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/gmap.idba.err.log.

Any idea how I can make rnaquast to recognize gmap? I tried to add the path to my ~/.bash_profile like export PATH=$PATH:/home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/gmap but I dont know why is not working. I am using a slurm script to initiate rnaquest.py:

!/bin/bash

SBATCH --job-name=test

SBATCH --partition=fat

SBATCH --time=96:00:00 #00:30:00

SBATCH --qos=large

SBATCH --cpus-per-task=36

SBATCH --mem=475G

SBATCH --output=test.out

SBATCH --error=test.err

source ~/.bash_profile source ~/ownSoft/miniconda3/etc/profile.d/conda.sh

export LANGUAGE=en_US.UTF-8 export LANG=en_US.UTF-8 export LC_ALL=en_US.UTF-8

conda activate /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast

srun rnaQUAST.py --test

conda deactivate

but that did not help either. Any ideas are much appreciated!

Magda

bernt-matthias commented 3 years ago

If you add something to PATH then it should be the directory containing the binary, i.e. /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/. But this should not be necessary with the activated conda env.

Also wondering why you use srun in your submission script.

Can you try to activate the conda env and execute gmap, /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast/bin/gmap, which gmap?

For the creation of the conda env conda create -c conda-forge -c bioconda -n rnaquast rnaquast should be sufficient. In case conda insists to install the 2021 version of gmap then you may add "gmap<2021.02.22".

mmcardozo commented 3 years ago

I did conda create -c conda-forge -c bioconda -n rnaquast rnaquast "gmap<2021.02.22" but got this:

conda activate /home/ollie/mcardozo/ownSoft/miniconda3/envs/rnaquast (rnaquast) mcardozo@ollie0:~/ownSoft/miniconda3/envs/rnaquast/bin$ which gmap ~/ownSoft/miniconda3/envs/rnaquast/bin/gmap

when I run the test still doesnt regonize it:

rnaQUAST: 2.2.0

System information: OS: Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-glibc2.17 (linux_64) Python version: 3.9.2 CPUs number: 28

External tools: matplotlib: 3.4.1 joblib: 1.0.1 gffutils: 0.10.1 blastn: 2.11.0+ makeblastdb: 2.11.0+ gmap: unknown

Started: 2021-04-13 11:03:27

How can I check that is the version I needed? Thanks again for your help! I'm new to this

bernt-matthias commented 3 years ago

gmap --version

output for me is

Note: gmap.avx2 does not exist.  For faster speed, may want to compile package on an AVX2 machine
GMAP version 2020-10-14 called with args: gmap.sse42 --version

GMAP: Genomic Mapping and Alignment Program
Part of GMAP package, version 2020-10-14
Build target: x86_64-conda-linux-gnu
Features: pthreads enabled, no alloca, zlib available, mmap available, littleendian, sigaction available, 64 bits available
Popcnt: mm_popcnt builtin_popcount
Builtin functions: builtin_clz builtin_ctz builtin_popcount
SIMD functions compiled: SSE2 SSSE3 SSE4.1 SSE4.2
Sizes: off_t (8), size_t (8), unsigned int (4), long int (8), long long int (8)
Default gmap directory (compiled): /home/berntm/miniconda3/envs/__rnaquast@2.2.0/share
Default gmap directory (environment): /home/berntm/miniconda3/envs/__rnaquast@2.2.0/share
Thomas D. Wu, Genentech, Inc.
Contact: twu@gene.com

You can also list all installed packages in the env

conda env export -n rnaquast

or

cat ~/ownSoft/miniconda3/envs/rnaquast/conda-meta/history

asl commented 3 years ago

IMO, it's highly likely that gmap conda package is broken: in particular it is compiled on the system with newer instruction set available and therefore it cannot be run on the systems w/o them. I would suggest to report this issue to Conda maintainers

bernt-matthias commented 3 years ago

@asl this is well possible. Lets see what the output of gmap --version is for @mmcardozo . I guess rnaQUAST decides on the usability of gmap based on this output, or?

asl commented 3 years ago

Tagging @andrewprzh @letovesnoi

mmcardozo commented 3 years ago

with conda env export -n rnaquast I found

gmap=2020.10.14=pl526h2f06484_0

but with which gmap --version

GNU which v2.20, Copyright (C) 1999 - 2008 Carlo Wood. GNU which comes with ABSOLUTELY NO WARRANTY; This program is free software; your freedom to use, change and distribute this program is protected by the GPL.

and with cat ~/ownSoft/miniconda3/envs/rnaquast/conda-meta/history

+bioconda/linux-64::gmap-2020.10.14-pl526h2f06484_0

bernt-matthias commented 3 years ago

Just gmap --version not which gmap --version

mmcardozo commented 3 years ago

sorry, nothing comes up with gmap --version

bernt-matthias commented 3 years ago

Can you execute echo $? directly after gmap --version ?

What kind of OS are you using?

mmcardozo commented 3 years ago

I get 255 I am using the Ollie Cray CS400 system from AWI, they use the Linux operating system CentOS and batch system SLURM

mmcardozo commented 3 years ago

UPDATE: for me it seems to work. I did the following to re-install rnaquast:

source ~/ownSoft/Anaconda3/etc/profile.d/conda.sh  
conda create -n rnaquast python=3.7 pip rnaquast=2.2.0 idba matplotlib "gmap<2021.02.22"

I was able to run the test without issue:

/home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/rnaQUAST.py --transcripts /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/idba.fasta /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/Trinity.fasta /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/spades.311.fasta --reference /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa --gtf /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/Saccharomyces_cerevisiae.R64-1-1.75.gtf --output_dir /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output --disable_infer_genes --disable_infer_transcripts

rnaQUAST: 2.2.0

System information:
  OS: Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-centos-7.5.1804-Core (linux_64)
  Python version: 3.7.10
  CPUs number: 36

External tools:
  matplotlib: 3.4.1
  joblib: 1.0.1
  gffutils: 0.10.1
  blastn: 2.11.0+
  makeblastdb: 2.11.0+
  gmap: 2020-10-14

Started: 2021-05-05 14:24:37

Logging to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/rnaQUAST.log

NOTICE: Maximum number of threads is set to 16 (use --threads option to set it manually)

2021-05-05 14:24:37
Getting reference...
Done.
Using non strand specific transcripts...

2021-05-05 14:24:38
Creating sqlite3 db by gffutils...
  saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Saccharomyces_cerevisiae.R64-1-1.75.db.

2021-05-05 14:24:43
Loading sqlite3 db by gffutils from /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Saccharomyces_cerevisiae.R64-1-1.75.db to memory...
Done.

2021-05-05 14:24:44
Getting GENE DATABASE metrics...
Done.

Sets maximum intron size equal 2583. Default is 1500000 bp.

2021-05-05 14:24:51
Sorting exons attributes...
  Sorted in I.
  Sorted in II.
  Sorted in III.
  Sorted in IV.
  Sorted in IX.
  Sorted in Mito.
  Sorted in V.
  Sorted in VI.
  Sorted in VII.
  Sorted in VIII.
  Sorted in X.
  Sorted in XI.
  Sorted in XII.
  Sorted in XIII.
  Sorted in XIV.
  Sorted in XV.
  Sorted in XVI.
Done.

  2021-05-05 14:24:52
  Getting transcripts from /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/idba.fasta...
  Done.

  2021-05-05 14:24:52
  Getting transcripts from /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/Trinity.fasta...
  Done.

  2021-05-05 14:24:52
  Getting transcripts from /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/spades.311.fasta...
  Done.

2021-05-05 14:24:52
Getting upper case fasta...
  saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.upper.fa

2021-05-05 14:24:52
Creating genome index by gmap_build...
  logs can be found in /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/gmap_build.out.log and /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/gmap_build.err.log.
  saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.upper

GMAP_BUILD TIME: 0:00:32.202855

2021-05-05 14:25:24
Aligning idba to Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.upper...
  log can be found in /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/gmap.idba.err.log.
  saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.psl

GMAP TIME: 0:00:08.717981

2021-05-05 14:25:33
Aligning Trinity to Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.upper...
  log can be found in /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/gmap.Trinity.err.log.
  saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.psl

GMAP TIME: 0:00:05.638409

2021-05-05 14:25:39
Aligning spades.311 to Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.upper...
  log can be found in /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/gmap.spades.311.err.log.
  saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.psl

GMAP TIME: 0:00:14.405834

2021-05-05 14:25:53
Extracting isoforms sequences...
Done.

2021-05-05 14:26:05
Getting blast database for /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.isoforms.fa
  saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.isoforms

2021-05-05 14:26:22
Transcripts:
  /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/idba.fasta -> idba
  /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/Trinity.fasta -> Trinity
  /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/spades.311.fasta -> spades.311
Reference:
  /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa
Gene coordinates:
  /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.cleared.gtf

Processing transcripts from /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/idba.fasta:

  2021-05-05 14:26:22
  Aligning /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/idba.fasta to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.isoforms by blastn...
    saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.blast6
    log can be found in /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/idba.blastn.log.

  2021-05-05 14:26:23
  Getting BLAST alignments report files...
    saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.assembled.best.blast6 (contains best alignments for assembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.paralogs.best.blast6 (contains best alignments for assembled transcripts having paralogs)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.misassembled.best.blast6 (contains best alignments for misassembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.misassembled.blast6 (contains all alignments for misassembled transcripts)

  2021-05-05 14:26:23
  Getting GMAP (or BLAT) alignments report files...
    saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.assembled.best.psl (contains best alignments for assembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.uniquely.psl (contains best alignments for uniquely aligned assembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.paralogs.best.psl (contains best alignments for assembled transcripts having paralogs)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.misassembled.best.psl (contains best alignments for misassembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/idba.misassembled.psl (contains all alignments for misassembled transcripts)

  2021-05-05 14:26:25
  Processing assembled aligned transcripts...
  Done.

  2021-05-05 14:26:43
  Processing misassembled aligned transcripts...
  Done.

  2021-05-05 14:26:43
  Processing misassembled aligned transcripts...
  Done.

  2021-05-05 14:26:43
  Getting BASIC TRANSCRIPTS metrics...
  Done.
  Getting ALIGNMENT metrics...
  Done.
  Getting SPECIFICITY metrics...
  Done.
  Getting SENSITIVITY metrics...
  Done.

Getting SEPARATED report for idba...

  2021-05-05 14:26:52
  Getting TXT report...
    Getting GENE DATABASE METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/database_metrics.txt
    Getting BASIC TRANSCRIPTS METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/basic_metrics.txt
    Getting ALIGNMENT METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/alignment_metrics.txt
    Getting ALIGNMENT METRICS FOR MISASSEMBLED (CHIMERIC) TRANSCRIPTS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/misassemblies.txt
    Getting ASSEMBLY COMPLETENESS (SENSITIVITY) report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/sensitivity.txt
    Getting ASSEMBLY SPECIFICITY report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/specificity.txt
  Done.

  2021-05-05 14:26:52
  Getting DISTRIBUTION report...
    Drawing cumulative transcript / isoform length plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/transcript_length.png
    Drawing cumulative blocks / exons length plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/block_length.png
    Drawing cumulative transcript aligned fraction plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/x-aligned.png
    Drawing cumulative number of blocks / exons per alignment / isoform plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/blocks_per_alignment.png
    Drawing cumulative alignment multiplicity plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/alignment_multiplicity.png
    Drawing cumulative substitution errors per alignment plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/mismatch_rate.png
    Drawing Nx plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/Nx.png
    Drawing NAx plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/NAx.png
    Drawing cumulative transcript matched fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/x-matched.png
    Drawing cumulative block matched fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/x-matched_blocks.png
    Drawing cumulative isoform assembled fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/x-assembled.png
    Drawing cumulative exon assembled fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/x-assembled_exons.png
    Drawing cumulative isoform covered fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/x-covered.png
    Drawing cumulative exon covered fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/x-covered_exons.png
    Drawing cumulative number of alignments per isoform plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/alignments_per_isoform.png
  Done.

  2021-05-05 14:26:56
  Getting OTHER reports...
    Getting Unaligned transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/idba.unaligned.fasta
    Getting Paralogous transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/idba.paralogs.fasta
    Getting Misassembled transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/idba.misassembled.fasta
    Getting Misassembled by BLAT transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/idba.misassembled.blat.fasta
    Getting Misassembled by BLASTN transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/idba.misassembled.blast.fasta
    Getting Unique aligned transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/idba.correct.fasta
    Getting Unannotated transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/idba.unannotated.fasta
    Getting fully assembled isoforms list...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/idba.95%-assembled.list
    Getting well assembled isoforms list...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output/idba.50%-assembled.list
  Done.

Processing transcripts from /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/Trinity.fasta:

  2021-05-05 14:26:56
  Aligning /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/Trinity.fasta to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.isoforms by blastn...
    saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.blast6
    log can be found in /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/Trinity.blastn.log.

  2021-05-05 14:26:57
  Getting BLAST alignments report files...
    saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.assembled.best.blast6 (contains best alignments for assembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.paralogs.best.blast6 (contains best alignments for assembled transcripts having paralogs)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.misassembled.best.blast6 (contains best alignments for misassembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.misassembled.blast6 (contains all alignments for misassembled transcripts)

  2021-05-05 14:26:57
  Getting GMAP (or BLAT) alignments report files...
    saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.assembled.best.psl (contains best alignments for assembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.uniquely.psl (contains best alignments for uniquely aligned assembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.paralogs.best.psl (contains best alignments for assembled transcripts having paralogs)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.misassembled.best.psl (contains best alignments for misassembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Trinity.misassembled.psl (contains all alignments for misassembled transcripts)

  2021-05-05 14:26:58
  Processing assembled aligned transcripts...
  Done.

  2021-05-05 14:27:14
  Processing misassembled aligned transcripts...
  Done.

  2021-05-05 14:27:14
  Processing misassembled aligned transcripts...
  Done.

  2021-05-05 14:27:14
  Getting BASIC TRANSCRIPTS metrics...
  Done.
  Getting ALIGNMENT metrics...
  Done.
  Getting SPECIFICITY metrics...
  Done.
  Getting SENSITIVITY metrics...
  Done.

Getting SEPARATED report for Trinity...

  2021-05-05 14:27:18
  Getting TXT report...
    Getting GENE DATABASE METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/database_metrics.txt
    Getting BASIC TRANSCRIPTS METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/basic_metrics.txt
    Getting ALIGNMENT METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/alignment_metrics.txt
    Getting ALIGNMENT METRICS FOR MISASSEMBLED (CHIMERIC) TRANSCRIPTS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/misassemblies.txt
    Getting ASSEMBLY COMPLETENESS (SENSITIVITY) report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/sensitivity.txt
    Getting ASSEMBLY SPECIFICITY report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/specificity.txt
  Done.

  2021-05-05 14:27:18
  Getting DISTRIBUTION report...
    Drawing cumulative transcript / isoform length plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/transcript_length.png
    Drawing cumulative blocks / exons length plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/block_length.png
    Drawing cumulative transcript aligned fraction plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/x-aligned.png
    Drawing cumulative number of blocks / exons per alignment / isoform plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/blocks_per_alignment.png
    Drawing cumulative alignment multiplicity plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/alignment_multiplicity.png
    Drawing cumulative substitution errors per alignment plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/mismatch_rate.png
    Drawing Nx plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Nx.png
    Drawing NAx plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/NAx.png
    Drawing cumulative transcript matched fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/x-matched.png
    Drawing cumulative block matched fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/x-matched_blocks.png
    Drawing cumulative isoform assembled fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/x-assembled.png
    Drawing cumulative exon assembled fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/x-assembled_exons.png
    Drawing cumulative isoform covered fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/x-covered.png
    Drawing cumulative exon covered fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/x-covered_exons.png
    Drawing cumulative number of alignments per isoform plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/alignments_per_isoform.png
  Done.

  2021-05-05 14:27:22
  Getting OTHER reports...
    Getting Unaligned transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Trinity.unaligned.fasta
    Getting Paralogous transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Trinity.paralogs.fasta
    Getting Misassembled transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Trinity.misassembled.fasta
    Getting Misassembled by BLAT transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Trinity.misassembled.blat.fasta
    Getting Misassembled by BLASTN transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Trinity.misassembled.blast.fasta
    Getting Unique aligned transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Trinity.correct.fasta
    Getting Unannotated transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Trinity.unannotated.fasta
    Getting fully assembled isoforms list...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Trinity.95%-assembled.list
    Getting well assembled isoforms list...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output/Trinity.50%-assembled.list
  Done.

Processing transcripts from /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/spades.311.fasta:

  2021-05-05 14:27:22
  Aligning /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/share/rnaquast-2.2.0-2/test_data/spades.311.fasta to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/Saccharomyces_cerevisiae.R64-1-1.75.isoforms by blastn...
    saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.blast6
    log can be found in /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/spades.311.blastn.log.

  2021-05-05 14:27:24
  Getting BLAST alignments report files...
    saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.assembled.best.blast6 (contains best alignments for assembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.paralogs.best.blast6 (contains best alignments for assembled transcripts having paralogs)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.misassembled.best.blast6 (contains best alignments for misassembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.misassembled.blast6 (contains all alignments for misassembled transcripts)

  2021-05-05 14:27:24
  Getting GMAP (or BLAT) alignments report files...
    saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.assembled.best.psl (contains best alignments for assembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.uniquely.psl (contains best alignments for uniquely aligned assembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.paralogs.best.psl (contains best alignments for assembled transcripts having paralogs)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.misassembled.best.psl (contains best alignments for misassembled transcripts)
             /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/tmp/spades.311.misassembled.psl (contains all alignments for misassembled transcripts)

  2021-05-05 14:27:26
  Processing assembled aligned transcripts...
  Done.

  2021-05-05 14:27:41
  Processing misassembled aligned transcripts...
  Done.

  2021-05-05 14:27:41
  Processing misassembled aligned transcripts...
  Done.

  2021-05-05 14:27:41
  Getting BASIC TRANSCRIPTS metrics...
  Done.
  Getting ALIGNMENT metrics...
  Done.
  Getting SPECIFICITY metrics...
  Done.
  Getting SENSITIVITY metrics...
  Done.

Getting SEPARATED report for spades.311...

  2021-05-05 14:27:47
  Getting TXT report...
    Getting GENE DATABASE METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/database_metrics.txt
    Getting BASIC TRANSCRIPTS METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/basic_metrics.txt
    Getting ALIGNMENT METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/alignment_metrics.txt
    Getting ALIGNMENT METRICS FOR MISASSEMBLED (CHIMERIC) TRANSCRIPTS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/misassemblies.txt
    Getting ASSEMBLY COMPLETENESS (SENSITIVITY) report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/sensitivity.txt
    Getting ASSEMBLY SPECIFICITY report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/specificity.txt
  Done.

  2021-05-05 14:27:47
  Getting DISTRIBUTION report...
    Drawing cumulative transcript / isoform length plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/transcript_length.png
    Drawing cumulative blocks / exons length plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/block_length.png
    Drawing cumulative transcript aligned fraction plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/x-aligned.png
    Drawing cumulative number of blocks / exons per alignment / isoform plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/blocks_per_alignment.png
    Drawing cumulative alignment multiplicity plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/alignment_multiplicity.png
    Drawing cumulative substitution errors per alignment plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/mismatch_rate.png
    Drawing Nx plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/Nx.png
    Drawing NAx plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/NAx.png
    Drawing cumulative transcript matched fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/x-matched.png
    Drawing cumulative block matched fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/x-matched_blocks.png
    Drawing cumulative isoform assembled fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/x-assembled.png
    Drawing cumulative exon assembled fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/x-assembled_exons.png
    Drawing cumulative isoform covered fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/x-covered.png
    Drawing cumulative exon covered fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/x-covered_exons.png
    Drawing cumulative number of alignments per isoform plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/alignments_per_isoform.png
  Done.

  2021-05-05 14:27:51
  Getting OTHER reports...
    Getting Unaligned transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/spades.311.unaligned.fasta
    Getting Paralogous transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/spades.311.paralogs.fasta
    Getting Misassembled transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/spades.311.misassembled.fasta
    Getting Misassembled by BLAT transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/spades.311.misassembled.blat.fasta
    Getting Misassembled by BLASTN transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/spades.311.misassembled.blast.fasta
    Getting Unique aligned transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/spades.311.correct.fasta
    Getting Unannotated transcripts report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/spades.311.unannotated.fasta
    Getting fully assembled isoforms list...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/spades.311.95%-assembled.list
    Getting well assembled isoforms list...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output/spades.311.50%-assembled.list
  Done.

2021-05-05 14:27:51
Getting COMPARISON report...

  2021-05-05 14:27:51
  Getting TXT report...
    Getting GENE DATABASE METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/database_metrics.txt
    Getting BASIC TRANSCRIPTS METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/basic_metrics.txt
    Getting ALIGNMENT METRICS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/alignment_metrics.txt
    Getting ALIGNMENT METRICS FOR MISASSEMBLED (CHIMERIC) TRANSCRIPTS report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/misassemblies.txt
    Getting ASSEMBLY COMPLETENESS (SENSITIVITY) report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/sensitivity.txt
    Getting ASSEMBLY SPECIFICITY report...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/specificity.txt
  Done.

  2021-05-05 14:27:51
  Getting DISTRIBUTION report...
    Drawing cumulative transcript / isoform length plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/transcript_length.png
    Drawing cumulative blocks / exons length plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/block_length.png
    Drawing cumulative transcript aligned fraction plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/x-aligned.png
    Drawing cumulative number of blocks / exons per alignment / isoform plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/blocks_per_alignment.png
    Drawing cumulative alignment multiplicity plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/alignment_multiplicity.png
    Drawing cumulative substitution errors per alignment plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/mismatch_rate.png
    Drawing Nx plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/Nx.png
    Drawing NAx plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/NAx.png
    Drawing cumulative transcript matched fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/x-matched.png
    Drawing cumulative block matched fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/x-matched_blocks.png
    Drawing cumulative isoform assembled fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/x-assembled.png
    Drawing cumulative exon assembled fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/x-assembled_exons.png
    Drawing cumulative isoform covered fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/x-covered.png
    Drawing cumulative exon covered fraction histogram...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/x-covered_exons.png
    Drawing cumulative number of alignments per isoform plot...
      saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output/alignments_per_isoform.png
  Done.
  saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output

2021-05-05 14:27:55
Getting SHORT SUMMARY report...
  saved to
    /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/short_report.txt
    /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/short_report.tex
    /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/short_report.pdf

THE QUALITY OF TRANSCRIPTOME ASSEMBLY DONE. RESULTS: /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output

Separated assemblies reports are saved to
  /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/idba_output
  /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/Trinity_output
  /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/spades.311_output
Comparison assemblies report are saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/comparison_output
  PDF version (tables and plots) saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/short_report.pdf
  TXT version (tables and plots) saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/short_report.txt

Log saved to /home/ollie/mcardozo/ownSoft/Anaconda3/envs/rnaquast/bin/rnaQUAST_test_output/logs/rnaQUAST.log

Finished: 2021-05-05 14:27:57
Elapsed time: 0:03:19.469757
NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0

Thank you for using rnaQUAST!

bernt-matthias commented 3 years ago

Thanks. I forgot to post that https://github.com/bioconda/bioconda-recipes/pull/27840 has "fixed" this.

Can you check if conda create -c bioconda -c conda-forge -n rnaquast rnaquast=2.2.0 also works (matplotlib should be installed automatically .. not sure about idba .. is this needed)?

mmcardozo commented 3 years ago

no, it did not:

conda create -c bioconda -c conda-forge -n rnaquast rnaquast=2.2.0

gives this:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                               

UnsatisfiableError: 
Note that strict channel priority may have removed packages required for satisfiability.

andrewprzh commented 3 years ago

Sorry for the huge delay, updated rnaQUAST to 2.2.1, big thanks to @bernt-matthias , this can be closed now, I guess!

ablab / rnaquast

idba segmentation fault #7

!/bin/bash

SBATCH --job-name=test

SBATCH --partition=fat

SBATCH --time=96:00:00 #00:30:00

SBATCH --qos=large

SBATCH --cpus-per-task=36

SBATCH --mem=475G

SBATCH --output=test.out

SBATCH --error=test.err