Comments (3)
Hi, did you compile asgal before running it?
cd /SOFTWARES/asgalvm/galig/
make prerequisites
make
Since it cannot find salmon bin in that subdirectory I think that it won't find SpliceAwareAligner bin in /SOFTWARES/asgalvm/galig/
either.
Can you please check that?
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yes, i did!
I did install it from scratch as it is a shared resource, so I made a python3 virtual environment and the git cloned the galig into it. Compiled it using these commands followed by pip3 installing pandas, bio, pysam
module --quiet purge
# Load necessary module for building
module load Biopython/1.78-foss-2020a-Python-3.8.2
module load CMake/3.16.4-GCCcore-9.3.0
module load SAMtools/1.10-GCC-9.3.0
module load GCC/9.3.0
# Install Python dependencies
python -m pip install --user pysam gffutils pandas
# Build LEMON locally
tar -xf lemon-1.3.1.tar.gz
mkdir -p lemon-1.3.1/build
cd lemon-1.3.1/build
cmake -DCMAKE_INSTALL_PREFIX="$(pwd)/../../galig/lemon/compiled/" ..
make -j
make install
cd ../../
# Build sdsl-lite which is bundled with galig
cd galig/sdsl-lite/build
cmake -DCMAKE_INSTALL_PREFIX="$(pwd)/../../sdsl-lite/compiled/" ..
make -j
make install
cd ../../../
# Lastly build galig
cd galig
make -j
And I also did " make prerequisites" & make , and it seems to work
(asgalvm) [sakshisi@login-1 /sakshisi/VirtualENV/asgalvm/galig]$ make prerequisites
* Salmon
--2021-03-11 18:39:42-- https://github.com/COMBINE-lab/salmon/releases/download/v0.12.0/salmon-0.12.0_linux_x86_64.tar.gz
Resolving github.com (github.com)... 140.82.121.3
Connecting to github.com (github.com)|140.82.121.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-releases.githubusercontent.com/32549942/531ac100-f8ed-11e8-9aa1-a1bc5fef457f?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210311%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210311T173942Z&X-Amz-Expires=300&X-Amz-Signature=dd638c237f0786c10edc6c9cf131a7cb24dc6ec53b2bded3f5775cb74f6865b1&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=32549942&response-content-disposition=attachment%3B%20filename%3Dsalmon-0.12.0_linux_x86_64.tar.gz&response-content-type=application%2Foctet-stream [following]
--2021-03-11 18:39:42-- https://github-releases.githubusercontent.com/32549942/531ac100-f8ed-11e8-9aa1-a1bc5fef457f?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210311%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210311T173942Z&X-Amz-Expires=300&X-Amz-Signature=dd638c237f0786c10edc6c9cf131a7cb24dc6ec53b2bded3f5775cb74f6865b1&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=32549942&response-content-disposition=attachment%3B%20filename%3Dsalmon-0.12.0_linux_x86_64.tar.gz&response-content-type=application%2Foctet-stream
Resolving github-releases.githubusercontent.com (github-releases.githubusercontent.com)... 185.199.108.154, 185.199.111.154, 185.199.109.154, ...
Connecting to github-releases.githubusercontent.com (github-releases.githubusercontent.com)|185.199.108.154|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 36791080 (35M) [application/octet-stream]
Saving to: ‘salmon-0.12.0_linux_x86_64.tar.gz’
100%[====================================================================================================>] 36,791,080 10.7MB/s in 3.5s
2021-03-11 18:39:46 (10.2 MB/s) - ‘salmon-0.12.0_linux_x86_64.tar.gz’ saved [36791080/36791080]
(asgalvm) [sakshisi@login-1/sakshisi/VirtualENV/asgalvm/galig]$ make
make[1]: Nothing to be done for `all'.
On running asgal sbatch script, salmon quasi indexing and mapping seems to work okay but samtools sorting shows some error
Traceback (most recent call last):
File "/cluster/work/users/sakshisi/VirtualENV/asgalvm/galig/asgal", line 585, in <module>
main()
File "/cluster/work/users/sakshisi/VirtualENV/asgalvm/galig/asgal", line 576, in main
runSalmon(args)
File "/cluster/work/users/sakshisi/VirtualENV/asgalvm/galig/asgal", line 210, in runSalmon
command_check_return(salmon_quant_cmd, salmonBam, salmonQuantLog, shell=True, verbose=args.verbose)
File "/cluster/work/users/sakshisi/VirtualENV/asgalvm/galig/asgal", line 62, in command_check_return
completed_process.check_returncode()
File "/cluster/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/subprocess.py", line 444, in check_returncode
raise CalledProcessError(self.returncode, self.args, self.stdout,
subprocess.CalledProcessError: Command '/cluster/work/users/sakshisi/VirtualENV/asgalvm/galig/salmon/bin/salmon quant -p 2 -i /sakshisi/VirtualENV/asgalvm/output/R01/salmon/salmon_index -l A -1 /sakshisi/U2OS/u2os_rawdata/X204SC20113963-Z01-F001/raw_data/R01/R01_1_val_1.fq.gz -2 /sakshisi/U2OS/u2os_rawdata/X204SC20113963-Z01-F001/raw_data/R01/R01_2_val_2.fq.gz -o /sakshisi/VirtualENV/asgalvm/output/R01/salmon/salmon_out --no-version-check --validateMappings --writeMappings --writeUnmappedNames | samtools view -Sb - | samtools sort -' returned non-zero exit status 127.
Thanks in advance for your help
best
SA
from galig.
Are the two directories containing the executables
(ie /cluster/work/users/sakshisi/VirtualENV/asgalvm/galig
and /cluster/work/users/sakshisi/VirtualENV/asgalvm/galig/salmon/bin/
)
in your $PATH
?
Can you try adding them and rerun asgal?
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Related Issues (16)
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