Align issue "Failed in RunDBS_1.pl! at /usr/local/vast-tools/bin/RunDBS_1.pl"

[neusmf]

Hi, I am trying to run align but I got an error. I try it using the container and also with the software on the path, and in all cases I had the same problem. I think that is similar to Issue#67.

Here you have the error log: readline() on closed filehandle VERSION at /usr/local/bin/vast-tools line 65. Use of uninitialized value $version in scalar chomp at /usr/local/bin/vast-tools line 66. readline() on closed filehandle VERSION at /usr/local/vast-tools/bin/RunDBS_1.pl line 261. Use of uninitialized value $version in scalar chomp at /usr/local/vast-tools/bin/RunDBS_1.pl line 262. [vast align]: VAST-TOOLS vNo version found [vast align]: Species assembly: hg38, VASTDB Species key: Hs2 [vast align]: VASTDB Version: vastdb.hs2.23.06.20 [vast align]: Input RNA-seq file(s): /fasterqcdump_output/SRR6916959_1.fastq.gz and /fasterqcdump_output/SRR6916959_2.fastq.gz [vast align]: Most common read lengths detected for fq1 & fq2: 96 (100.00%) and 96 (100.00%) [vast align]: Sample name: SRR6916959_1 [vast align]: Using VASTDB -> /01_Vast-tools_C/Hs2 [vast align]: Setting output directory to test [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to 01_Vast-tools_C/test/tmp!

reads processed: 500000

reads with at least one reported alignment: 346874 (69.37%)

reads that failed to align: 138413 (27.68%)

reads with alignments suppressed due to -m: 14713 (2.94%)

Reported 346874 alignments to 1 output stream(s) [vast align]: fraction of first reads mapping to fwd / rev strand : 0.5211 / 0.4789

reads processed: 500000

reads with at least one reported alignment: 343039 (68.61%)

reads that failed to align: 142475 (28.50%)

reads with alignments suppressed due to -m: 14486 (2.90%)

Reported 343039 alignments to 1 output stream(s) [vast align]: fraction of second reads mapping to fwd / rev strand : 0.5161 / 0.4839 [vast align]: Mapping RNAseq reads against mRNA sequences [vast align]: Calculating cRPKMs Modification of non-creatable array value attempted, subscript -7 at /usr/local/vast-tools/bin/expr_RPKM.pl line 43, <> line 9494512. Error while flushing and closing output terminate called after throwing an instance of 'int' Aborted (core dumped) [vast align error]: gzip -dc /fasterqcdump_output/SRR6916959_1.fastq.gz | /usr/local/vast-tools/bin/Trim.pl --once --targetLen 50 -v | bowtie -q -5 0 -p 8 -m 1 -v 2 01_Vast-tools_C/Hs2/EXPRESSION/mRNA - | /usr/local/vast-tools/bin/expr_RPKM.pl - /01_Vast-tools_C/Hs2/EXPRESSION/Hs2_mRNA-50.eff expr_out/SRR69169 59_1 > expr_out/SRR6916959_1.cRPKM Failed in RunDBS_1.pl! at /usr/local/vast-tools/bin/RunDBS_1.pl line 207.

Thanks in advance, Neus

[mirimia]

Hi Neus,

I think it might be an issue with the folder structure or permissions.

How did you run align? (The full command).

Thanks

[neusmf]

Hi, I used the following command: vast-tools align --dbDir ./ /fasterqcdump_output/SRR6916959_1.fastq.gz /fasterqcdump_output/SRR6916959_2.fastq.gz -o test -c 8 -sp Hs2

When I run it in the container then I run: "singularity exec ./vast-tools.sif ./align_test.sh", where I have the command above in align_test.sh

Thanks, Neus

[mirimia]

Can you try deleting

--dbDir ./

?

[neusmf]

Thanks! It worked!