abyss-pe is aborted after 20 30 minutes

[angelogava]

Hello everyone,

I'm having trouble using abyss-pe, perhaps because I'm new to this tool.

When I use abyss-pe without setting B, it terminates and generates scaffold files.

However, when I set B in order to use Bloom filter mode, it aborts at a certain point.

Below is the full log when I used v=-vv.

Command:
abyss-pe name=BTI5 k=90 B=6G in='BTI5_CKDN230000708-1A_HT5FKDSX5_L2_1_uniq1.fastq BTI5_CKDN230000708-1A_HT5FKDSX5_L2_1_uniq2.fastq' v=-vv

Log:

abyss-rresolver-short -vv -b6G -j2 -k90  \
-h BTI5-1-rr --dot -c BTI5-1-rr.fa -g BTI5-1-rr.dot BTI5-1.fa BTI5-1.dot BTI5_CKDN230000708-1A_HT5FKDSX5_L2_1_uniq1.fastq BTI5_CKDN230000708-1A_HT5FKDSX5_L2_1_uniq2.fastq 

Loading contig graph from BTI5-1.dot'... Contig graph loaded. V=85166 E=129400 E/V=1.52`

Degree: ▁▇█▁
        01234

0: 13% 1: 34% 2-4: 53% 5+: 0% max: 4
Loading contigs from BTI5-1.fa'... Contigs loaded. Determining read stats... '**cat: standard output: No such file or directory**

**[2025-02-21 22:09:51][WARNING] BTI5_CKDN230000708-1A_HT5FKDSX5_L2_1_uniq2.fastq is empty.**

cat: standard output: No such file or directory

'Helper process failed before data stream was closed:'

'PID 15125 exited with status 1'

'[2025-02-21 22:09:51][ERROR] Error communicating with helper process.'

'[2025-02-21 22:09:51][WARNING] BTI5_CKDN230000708-1A_HT5FKDSX5_L2_1_uniq1.fastq is empty.'

'make: *** [/usr/bin/abyss-pe:569: BTI5-1-rr.dot] Erro 1'

[jwcodee]

Hi, thanks for your interest in using ABySS. I'd like to just confirm that both 'BTI5_CKDN230000708-1A_HT5FKDSX5_L2_1_uniq1.fastq BTI5_CKDN230000708-1A_HT5FKDSX5_L2_1_uniq2.fastq' are in your current directory and are non empty.

[angelogava]

yes, the files are in the working directory and are 4.2GB each... abyss-pe can perform the assembly and read all sequences, then aborts

[angelogava]

Just to give more details about my problem...

The first time I run abyss-pe, the entire process detailed in the log file (abyss-pe.log) that I am attaching happens.

abyss-pe.log

If I run it a second time, with the same 'name', I believe it uses the files already mounted and generates the error log that I put in my first comment...

[jwcodee]

Yes, you should use another name or just start fresh in another directory, The way the makefile works is it restarts from the previous steps that completed successfully but in this case the two different modes might not be fully compatible and could potentially contribute to this issue you are seeing.