search

alekseyzimin / EviAnn_release

This is the standalone version of the EviAnn pipeline
GNU General Public License v3.0
15 stars 1 forks source link

Issue when using multiple bam files as inputs #6

Closed ko0000 closed 3 months ago

ko0000 commented 3 months ago

Greeting,

I am trying to run EviAnn software using the bam file (single-end RNA-seq aligned to the softmasked genome)

Below is the command I ran

./EviAnn-1.0.8/bin/eviann.sh \
        -t 5 \
    -g /home/08_eviann/PRJNA666745.WBPS18.genomic_softmasked.fa \
    -u /home/08_eviann/bam.txt \
    -r /home/02-Braker/proteins.fa

However, I encountered this error 

 Must specify at least one non-empty file with filenames of RNAseq reads with -p or -u or a file with ESTs from the same or closely related species with -e

Here is my “bam.txt”

/home/reannotation/01-GEMmaker/results/Samples/CAG_1_1/CAG_1_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_1_2/CAG_1_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_2_1/CAG_2_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_2_2/CAG_2_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_3_1/CAG_3_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_3_2/CAG_3_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_4_1/CAG_4_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_4_2/CAG_4_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_5_1/CAG_5_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_5_2/CAG_5_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_6_1/CAG_6_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/CAG_6_2/CAG_6_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R1_trimmed_1/R1_trimmed_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R1_trimmed_2/R1_trimmed_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R2_trimmed_1/R2_trimmed_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R2_trimmed_2/R2_trimmed_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R3_trimmed_1/R3_trimmed_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R3_trimmed_2/R3_trimmed_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R4_trimmed_1/R4_trimmed_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R4_trimmed_2/R4_trimmed_2.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R5_trimmed_1/R5_trimmed_1.sorted.bam bam
/home/reannotation/01-GEMmaker/results/Samples/R5_trimmed_2/R5_trimmed_2.sorted.bam bam

I can confirm that the absolute paths are correct and all bam files are not empty.

What could be the problem?

Many thanks,

Ko

alekseyzimin commented 3 months ago

Hi,

Please specify the bam.txt with -p not with -u, should work.

Best, Aleksey

On Tue, Apr 30, 2024 at 1:20 AM Ko @.***> wrote:

Greeting,

I am trying to run EviAnn software using the bam file (single-end RNA-seq aligned to the softmasked genome)

Below is the command I ran

./EviAnn-1.0.8/bin/eviann.sh \ -t 5 \ -g /home/08_eviann/PRJNA666745.WBPS18.genomic_softmasked.fa \ -u /home/08_eviann/bam.txt \ -r /home/02-Braker/proteins.fa

However, I encountered this error

Must specify at least one non-empty file with filenames of RNAseq reads with -p or -u or a file with ESTs from the same or closely related species with -e

Here is my “bam.txt”

/home/reannotation/01-GEMmaker/results/Samples/CAG_1_1/CAG_1_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_1_2/CAG_1_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_2_1/CAG_2_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_2_2/CAG_2_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_3_1/CAG_3_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_3_2/CAG_3_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_4_1/CAG_4_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_4_2/CAG_4_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_5_1/CAG_5_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_5_2/CAG_5_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_6_1/CAG_6_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/CAG_6_2/CAG_6_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R1_trimmed_1/R1_trimmed_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R1_trimmed_2/R1_trimmed_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R2_trimmed_1/R2_trimmed_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R2_trimmed_2/R2_trimmed_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R3_trimmed_1/R3_trimmed_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R3_trimmed_2/R3_trimmed_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R4_trimmed_1/R4_trimmed_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R4_trimmed_2/R4_trimmed_2.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R5_trimmed_1/R5_trimmed_1.sorted.bam bam /home/reannotation/01-GEMmaker/results/Samples/R5_trimmed_2/R5_trimmed_2.sorted.bam bam

I can confirm that the absolute paths are correct and all bam files are not empty.

What could be the problem?

Many thanks,

Ko

— Reply to this email directly, view it on GitHub https://github.com/alekseyzimin/EviAnn_release/issues/6, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXGHPJUI3RPMORR6FUURTY74S25AVCNFSM6AAAAABG7RO5MOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI3TANJSHAZTGOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

ko0000 commented 3 months ago

Thank you Aleksey. It does work. In future, should i used -p flag instead of -u for bam files (even if the bam files are from unpaired RNA-seq reads) ?

alekseyzimin commented 3 months ago

Yes, please use -p for all BAM file records. For BAM files, the processing is the same for paired and unpaired. I will add this to the user's guide.

On Tue, Apr 30, 2024 at 5:25 PM Ko @.***> wrote:

Thank you Aleksey. It does work. In future, should i used -p flag instead of -u for bam files (even if the bam files are from unpaired RNA-seq reads) ?

— Reply to this email directly, view it on GitHub https://github.com/alekseyzimin/EviAnn_release/issues/6#issuecomment-2087377896, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXGHORZN3KTFOI2F2R2BDZAAD3TAVCNFSM6AAAAABG7RO5MOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBXGM3TOOBZGY . You are receiving this because you commented.Message ID: @.***>

-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

ko0000 commented 3 months ago

okay. Thanks!