I was running RNACocktail for RNA quantification using shell command below:
# ${SRR} stands for SRR accession of the sample
run_rnacocktail.py quantify \
--quantifier_idx /home/data/refdir/index/salmon/hg38_index \
--1 ./sra/${SRR}_1.fastq.gz \
--2 ./sra/${SRR}_2.fastq.gz \
--libtype IU \
--outdir ./sra/out \
--workdir ./sra/work \
--threads 10 \
--sample ${SRR} \
--unzip
I built all salmon versions above 0.11.0 from source only to find that option '-k' failed to be recognised by command salmon quant. The outputs were the same in every version of salmon and in every salmon_smem.log of samples it processed:
Exception : [unrecognised option '-k']. Exiting.
Below is the command line output:
INFO 2021-06-06 20:51:29,182 src.run_quantify --------------------------STEP 1--------------------------
INFO 2021-06-06 20:51:29,183 src.run_quantify Task: Salmon-SMEM for SRR10435206
INFO 2021-06-06 20:51:29,183 src.run_quantify Running "bash -c salmon quant -i /home/data/refdir/index/salmon/hg38_index -p 10 -k 19 -l IU -1 <(gunzip -c ./sra/SRR10435206_1.fastq.gz) -2 <(gunzip -c ./sra/SRR10435206_2.fastq.gz) -o ./sra/work/salmon_smem/SRR10435206"
INFO 2021-06-06 20:51:29,543 src.run_quantify Returned code 1 (0.357945 seconds)
ERROR 2021-06-06 20:51:29,543 src.run_quantify Aborting!
INFO 2021-06-06 20:51:29,543 src.run_quantify Salmon-SMEM failed!
ERROR 2021-06-06 20:51:29,543 src.run_quantify Failed Salmon-SMEM for SRR10435206. Log file: ./sra/work/salmon_smem/SRR10435206/salmon_smem.log
As stated in your Github page, salmon version of 0.11.0 worked fine, instead.
When it comes to RNACocktail, I guess it is time for it to move on and adopt a salmon version newer than 0.11.0, at least 0.11.1, as the feature of option '-k' recognition is almost obsolete as aforementioned. Installation of salmon version 0.11.0 from Conda is also discouraged with the advent of libtbb issue:
error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory
(ERR): Description of arguments failed!
ldd shows libtbb refers to no .so file on the server.
Obviously salmon version 0.11.0 is badly off and seriously ill. Please let it rest in peace as you are maintaining RNACocktail at least up to 11 Nov 2020, only 7 months away from my issue arousal, inferred from date of your latest release.
Alternatively, you can modify the Python code to detect the version of salmon to avoid feeding option '-k' into salmon quant of version above 0.11.0, which seems to be the simplest and compatible solution.
Anyway I greatly appreciate your efforts in developing such a versatile tool to simplify RNA-seq analysis. You've done such a great job! I wish you are still actively maintaining this tool.
I was running RNACocktail for RNA quantification using shell command below:
I built all salmon versions above 0.11.0 from source only to find that option '-k' failed to be recognised by command
salmon quant. The outputs were the same in every version of salmon and in everysalmon_smem.logof samples it processed:Below is the command line output:
As stated in your Github page, salmon version of 0.11.0 worked fine, instead. When it comes to RNACocktail, I guess it is time for it to move on and adopt a salmon version newer than 0.11.0, at least 0.11.1, as the feature of option '-k' recognition is almost obsolete as aforementioned. Installation of salmon version 0.11.0 from Conda is also discouraged with the advent of libtbb issue:
lddshows libtbb refers to no .so file on the server. Obviously salmon version 0.11.0 is badly off and seriously ill. Please let it rest in peace as you are maintaining RNACocktail at least up to 11 Nov 2020, only 7 months away from my issue arousal, inferred from date of your latest release. Alternatively, you can modify the Python code to detect the version of salmon to avoid feeding option '-k' intosalmon quantof version above 0.11.0, which seems to be the simplest and compatible solution. Anyway I greatly appreciate your efforts in developing such a versatile tool to simplify RNA-seq analysis. You've done such a great job! I wish you are still actively maintaining this tool.