FastQ gzipped files not accepted as input?

[auesro]

Please report

• [ ] version of RNA-Bloom with java -jar RNA-Bloom.jar -version Previous command results in: Error: Unable to access jarfile RNA-Bloom.jar So command used for RNA-Bloom version: rnabloom -v RNA-Bloom v1.4.3 Ka Ming Nip, Canada's Michael Smith Genome Sciences Centre, BC Cancer Copyright 2018-present

• [ ] version of java with java -version openjdk version "11.0.13" 2021-10-19 OpenJDK Runtime Environment JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21) OpenJDK 64-Bit Server VM JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21, mixed mode)

• [ ] exact command used to run RNA-Bloom rnabloom -pool readslist.txt -revcomp-right -ntcard -t 10 -mergepool -outdir /home/auesro/Desktop/RNA_Bloom/output -k 20

Error:

RNA-Bloom v1.4.3
args: [-pool, readslist.txt, -revcomp-right, -ntcard, -t, 10, -mergepool, -outdir, /home/auesro/Desktop/RNA_Bloom/output, -k, 20]

name:   rnabloom
outdir: /home/auesro/Desktop/RNA_Bloom/output
Pooled assembly mode is ON!
Parsing pool reads list file `readslist.txt`...
ERROR: Unsupported file format detected in input file `left`. Only FASTA and FASTQ formats are supported.
rnabloom.io.FileFormatException: Unsupported file format detected in input file `left`. Only FASTA and FASTQ formats are supported.
    at rnabloom.RNABloom.checkInputFileFormat(RNABloom.java:344)
    at rnabloom.RNABloom.main(RNABloom.java:6357)

My fastq files are gzipped but according to the Readme.md, gzip compression is supported warning Input reads must be in either FASTQ or FASTA format and may be compressed with GZIP.

Any ideas?

Thanks!

A

[kmnip]

Can you please report the first 10 lines of your readslist.txt? You get that error when the read file you specified is not a FASTA/FASTQ file.

[auesro]

Sure, only 3 lines though:

#name left right
C1 /home/LAB/lab_eh_2/AER_Data/snRNAseq/C1/trimmed/A_S1_L001_R1_001_val_1.fq.gz /home/LAB/lab_eh_2/AER_Data/snRNAseq/C1/trimmed/A_S1_L001_R2_001_val_2.fq.gz
C2 /home/LAB/lab_eh_2/AER_Data/snRNAseq/C2/trimmed/C_S1_L001_R1_001_val_1.fq.gz /home/LAB/lab_eh_2/AER_Data/snRNAseq/C2/trimmed/C_S1_L001_R2_001_val_2.fq.gz

Yes, I know, my read files are gz compressed FASTQ files and according to your instructions, input reads can be gz compressed. But I still get that error...

[kmnip]

Ahh, you just need to remove the first line. That will be supported in an upcoming release.

[auesro]

Ohhh You mean I need to remove #name left right line from the readlist.txt file?

[kmnip]

Yes. That formatting is meant for the code in the master branch. If you look at the README that came with version 1.4.3, it is not there. Sorry for the confusion!

[auesro]

I see! Thats great, easy to fix.

One last question: I just noticed you are also an author at the TransAbyss package...would you recommend TransAbyss or RNA-Bloom for de novo transcriptome assembly from scRNAseq data?

[kmnip]

Please use RNA-Bloom for both single-cell and bulk RNA-seq data. Thanks!

[auesro]

Will do! Thanks for your help!