File name is changing abnormally after running sortmerna

[SA-Park]

Hello, Thanks for great tool!

I'm writing this post to inform you something weird.
I set input file name as "PRO_Dis3_0h_r1_1.fastq_100bp.fq".
Then I run this commend :

sortmerna
--ref $rRNA_path/rfam-5.8s-database-id98.fasta
--ref $rRNA_path/rfam-5s-database-id98.fasta
--ref $rRNA_path/silva-euk-18s-id95.fasta
--ref $rRNA_path/silva-euk-28s-id98.fasta
--reads $WD/01_Trim_100bp/PRO_Dis3_0h_r1_1.fastq_100bp.fq
--num_alignments 1 --fastx
--aligned $WD/02_sortmerna/aligned/PRO_Dis3_0h_r1_1.fastq_aligned.fq
--other $WD/02_sortmerna/unaligned/PRO_Dis3_0h_r1_1.fastq_unaligned.fq
-v --threads 14
--kvdb $WD/02_sortmerna/kvdb/PRO_Dis3_0h_r1_1.fastq_kvdb
--idx-dir $WD/02_sortmerna/index/PRO_Dis3_0h_r1_1.fastq_index
-workdir $WD/02_sortmerna

And I got the following outputs....

PRO_Dis3_0h_r1_1.fastq_aligned.fq.log
PRO_Dis3h_r1_1.fastq_aligned.fq_0.fq
[directory] PRO_Dis3_0h_r1_1.fastq_index
[directory] PRO_Dis3_0h_r1_1.fastq_kvdb
PRO_Dis3h_r1_1.fastq_unaligned.fq_0.fq

aligned & unaligned output file name got altered!
Name of other files which don't contain "_0" didn't altered.

In execution trace, the name changed at [merge:83].
I attached the execution trace log txt file here
220109_sortmerna_excute.txt

I avoided this by simply changing the file name, but I decided to provide this information for others.
Hope this is helpful for you.

[biocodz]

Hi @SA-Park.
Thanks for reporting this bug.
Because the file names are complex, the logic broke while renaming the final output. Instead of removing the last '0' in the name, it removed the first one found.
We'll fix this in the next release

[RaverJay]

This is still broken for me, running SortMeRNA version 4.3.4

Command:
    sortmerna --ref /data/fass1/database/sortmerna/rRNA_databases//rfam-5s-database-id98.fasta --ref /data/fass1/database/sortmerna/rRNA_databases//rfam-5.8s-database-id98.fasta --ref /data/fass1/database/sortmerna/rRNA_databases//silva-euk-18s-id95.fasta --ref /data/fass1/database/sortmerna/rRNA_databases//silva-euk-28s-id98.fasta --ref /data/fass1/database/sortmerna/rRNA_databases//hsa_MT_rRNA_RNR1_RNR2.fasta --reads fastp/sRNA_tropho_single_05.fq --fastx --threads 40 -m 8000 -v --workdir sortmerna/sRNA_tropho_single_05 --aligned sortmerna/sRNA_tropho_single_05_aligned --other sortmerna/sRNA_tropho_single_05_other

yields:

folder sRNA_tropho_single_05
file sRNA_tropho_single_05_aligned.log
but
sRNA_tropho_single5_aligned_0.fq
sRNA_tropho_single5_other_0.fq

[biocodz]

The fix will be included in release 4.3.6 (soon)

[biocodz]

fixed in v4.3.6