Closed ko0000 closed 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
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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) ?
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) ?
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-- 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
okay. Thanks!
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
However, I encountered this error
Here is my “bam.txt”
I can confirm that the absolute paths are correct and all bam files are not empty.
What could be the problem?
Many thanks,
Ko