No results in mapped to any database

[SergioRodLla]

Hi !

I am running sports1.1 with the following command:

DIR=/media/sergio/HDD1/smallrna sports.pl -i sports_pipeline/seq_address.txt -p 8 -g $DIR/features/SPORTS_db/Mus_musculus/genome/mm10/genome -m $DIR/features/SPORTS_db/Mus_musculus/miRBase/21/miRBase_21-mmu -r $DIR/features/SPORTS_db/Mus_musculus/rRNAdb/mouse_rRNA -t $DIR/features/SPORTS_db/Mus_musculus/GtRNAdb/mm10/mm10-tRNAs -w $DIR/features/SPORTS_db/Mus_musculus/piRBase/piR_mouse -e $DIR/features/SPORTS_db/Mus_musculus/Ensembl/release-89/Mus_musculus.GRCm38.ncrna -f $DIR/features/SPORTS_db/Mus_musculus/Rfam/12.3/Rfam-12.3-mouse -o sports_pipeline/output/ -k

Not that I'm ruinning Bowtie version 1.3.1 and I used Trimgalore to trim the read adapters.

Processed files are run very fasta and the processing report for every sample look like this, with no alignments in any database:

I guess that the message about the index comes from the more recent version of Bowtie. However I do not know where the "rm" error comes from. My "seq_address.txt" file looks like this:

Thank you in advance! Sergio

[junchaoshi]

Could you send the header of your .fasta file?

[SergioRodLla]

Thank you for the quick reply. The header looks like this:

>VH00268:107:AACKHFJM5:1:1101:19973:1000 1:N:0:AAGATCAT+ACGTTATT
GNGGCACCAACACTGCTCTGTAAGAGCAGCCT
>VH00268:107:AACKHFJM5:1:1101:20769:1000 1:N:0:AAGATCAT+ACGTTATT
GNGCCGCACGGAAATATTGGC
>VH00268:107:AACKHFJM5:1:1101:21450:1000 1:N:0:AAGATCAT+ACGTTATT
GNAGGTAGTAGGTTGTATAGTT
>VH00268:107:AACKHFJM5:1:1101:21753:1000 1:N:0:AAGATCAT+ACGTTATT
GNACCCTGTTTAAGGATCTGCTTGATGCTA
>VH00268:107:AACKHFJM5:1:1101:22018:1000 1:N:0:AAGATCAT+ACGTTATT
CNAGCAGAGGTAGATGGACTT

[junchaoshi]

Hi Sergio,

I can't replicate this problem. It might be because bowtie 1.3.0+ has changed the parameters for building the index. You can try manually building the bowtie index by following this format: "genome.[1-4, rev.1-2].ebwt[l]" for the .fa file named "genome", and then run SPORTS again. Another option is to use bowtie version <=1.2.3.

[SergioRodLla]

Hi,

I've tried using the raw fastq files and it worked fine. I will try your suggestion with bowtie. Thank you for the feedback.

[junchaoshi]

Glad to know you have solved the problem.