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Dear bacass community, I am new to bacass but wan...
# bacass
j
Dear bacass community, I am new to bacass but want to give it a try for a plasmid assembly. I generally have no issues running nf-core workflows on our local hpc (singularity) but everytime I try to run bacass I get the error shown in the picture. I feel is something related to java, but I am not sure. Has anyone seen anything like this? Any help would be appreciated . Thanks!
d
Hi!, I reproduced the command without any issues. Could you please share the error details form the 
.nextflow.log
file? it might provide a more detailed info about the issue. Another thing that may be related to the problem is the input samplesheet. This is the expected input format: TSV files:
Copy code
ID    R1    R2    LongFastQ    Fast5    GenomeSize
Sample1    /path/to/sample1_R1.fastq.gz    /path/to/sample1_R2.fastq.gz    NA    NA    3.1m
CSV files:
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ID,R1,R2,LongFastQ,Fast5,GenomeSize
Sample1,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz,NA,NA,3.1m
nextflow version 23.10.1.5891
Update: After conducting a fresh run, I observed that Prokka took longer than usual to download its singularity image, resulting in an 
error status 143
. While this may not be directly related, it's worth considering. I'll address this in 
dev
branch.
j
@Daniel_VM Thank you for you prompt reply! I am attaching the 
nextflow.log
file I hope this helps. Also, the TSV file I used was (my input file is in the same directory):
Copy code
ID     R1       R2      LongFastQ       Fast5   GenomeSize
shortreads      NA      NA      NA      NA      NA
longreads       NA      NA      TQSVYJ_1.fastq.gz       NA
shortNlong      NA      NA      NA      NA      NA
From you example I think I might not need to add the 
shortreads
and 
shortNlong
rows. Is 
GenomeSize
required? Thank you!
nextflow.log
Just realized I am missing a 
NA
on the 
longreads
row 🤦‍♂️. Fixing and running it again...nope, still the same error. UPDATE: I ran version 2.1.0 with no issues.
FINAL UPDATE: I neglected of mentioning that I am only using Nanopore long reads and It appears that you need to be explicit about what type of assembly you want. I re-ran version 
2.2.0
using the following command:
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nextflow run nf-core/bacass -r 2.2.0 --input samplesheet.csv -profile singularity -resume --outdir out/ --assembly_type long --assembler miniasm --kraken2db '<https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz>'
I came across with that solution because when I ran version 
2.1.0
, although it ran with no issues, it didn't output the assembly directory. Then I explicitly indicated the 
--assembly_type
and the 
--assembler
and got the results. So I tried this in version 
2.2.0
and it worked! I looked at the documentation and it seems there isn't a warning/note about this (unless I missed it). It might be beneficial adding something like this. @Daniel_VM Thank you for your time and please let me know if you have any questions!
d
Hi @Javi, Apologies for the late reply. Great work! I wanted to point out that you don't need to define the IDs 'shortreads' and 'shortNlong' since there are no input files for these lines. These IDs were added just to demonstrate which path is triggered based on the completion of the columns.
I think that it will be best to find a better example of input samplesheet in the bacass's 
readme.md
file 😅 .
Because the field ID corresponds to the sample name associated with the input files in columns R1, R2, LongFastQ, or Fast5
j
No worries! Aha! that makes sense! and because there was no actual input file it threw an error because it was looking for something that was 'empty'? But It still throws the same error when I only put the LongFastQ file in the samplesheet and not telling bacass that I want long-reads assembly only. So bacass do not 'guess' the type of the assembly based on the 
samplesheet
and always assumes you are using short reads (my guess).
d
Yes, it might be necessary to specify the assembly type by using the parameter: 
--assembly_type
j
@Daniel_VM Just as a follow-up, I wanted to let you know (and ask) that when using 
--assembler canu
, everything works but the assembly itself. Is this a known bug? or Do you know a work around this? I am able to use all the other assemblers except canu. Thank you!
d
Hi @Javi Thanks for reporting. I couldn't find any related issues on nf-core/bacass's github. Could you please share the log or errors?
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