Issue with "-mergepool" option

[mgabriel01]

Please report

• version of RNA-Bloom : RNA-Bloom v2.0.1
• version of java : openjdk 11.0.25 2024-10-15
• exact command used to run RNA-Bloom : java -Xmx5g -jar /home/marcgabriel/Downloads/RNA-Bloom_v2.0.1/RNA-Bloom.jar -pool /media/marcgabriel/saylar18/RNAbloom_results_5_cellLines/CCLE_pancreas_cellLines_rnabloom_desc.tsv --memory 10 -revcomp-right -t 20 -outdir /media/marcgabriel/saylar18/RNAbloom_results_5_cellLines/CCLE_pancreas_cellLines_rnabloom/ -length 30 -n CCLE_pancreas_cellLines -mergepool -prefix CCLE_pancreas_cellLines -chimera -norr

Hello,

I'm having issues with RNA-bloom, with the option "-mergepool" (I have 5 samples, and I would like to have at the end a merged file of transcripts, without redundancy) :

> Stage 2: Assemble fragments for 5 samples
>> Working on "ASPC1" (sample 1 of 5)...
WARNING: Fragments were already assembled for "ASPC1!
>> Fragments assembled in 0.001s

>> Working on "BXPC3" (sample 2 of 5)...
WARNING: Fragments were already assembled for "BXPC3!
>> Fragments assembled in 0.001s

>> Working on "CAPAN1" (sample 3 of 5)...
WARNING: Fragments were already assembled for "CAPAN1!
>> Fragments assembled in 0.0s

>> Working on "MIAPACA2" (sample 4 of 5)...
WARNING: Fragments were already assembled for "MIAPACA2!
>> Fragments assembled in 0.0s

>> Working on "PANC1" (sample 5 of 5)...
WARNING: Fragments were already assembled for "PANC1!
>> Fragments assembled in 0.0s

> Stage 2 completed in 0.014s

> Stage 3: Assemble transcripts for 5 samples
>> Working on "ASPC1" (sample 1 of 5)...
WARNING: Transcripts were already assembled for "ASPC1"!
Reducing redundancy in assembled transcripts...
Parsed 0 overlap records in 0.002s
before: 1,997,272	after: 1,997,272
ERROR: Error during redundancy reduction!

By checking the log file after the error, for the 1st sample, I can see this :

[ERROR] unknown option in "-e"

This is how my READSLIST.txt file looks like :

#name	left	right
ASPC1	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/ASPC1_2.trim.fastq.gz	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/ASPC1_1.trim.fastq.gz
BXPC3	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/BXPC3_2.trim.fastq.gz	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/BXPC3_1.trim.fastq.gz
CAPAN1	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/CAPAN1_2.trim.fastq.gz	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/CAPAN1_1.trim.fastq.gz
MIAPACA2	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/MIAPACA2_2.trim.fastq.gz	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/MIAPACA2_1.trim.fast
q.gz
PANC1	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/PANC1_2.trim.fastq.gz	/media/marcgabriel/saylar16/CEREUS_data_analysis_MM/trimmed_fastq/trim/PANC1_1.trim.fastq.gz

Thank you in advance for your help !

Marc G.

[kmnip]

Hi @mgabriel01 ,

I think this error message came from minimap2:

[ERROR] unknown option in "-e"

Can you please check your minimap2 version? and see whether the -e option is available in the help menu (via --help)?
If not, please update your minimap2 to the latest version.

[mgabriel01]

Hello,

Indeed I was using minimap2 v2.17 ; I did the update to the version v2.28 (latest to this day), and it went further. Do you know a way to speed it up (I'm already using 20 threads) ?

Thank you again for your fast answer !

Marc G.

[kmnip]

Sorry, I missed your last message. Did you manage to create the merged assembly?

[mgabriel01]

I had to disable the redundancy reduction with "-norr" finally, it took too long (it was still running after 3 days for the 1st sample)...