Trinity fails when dealing with very few reads

[Joon-Klaps]

Description of the bug

Trinity fails when dealing with very few reads and is unable to reconstruct a consensus genome.

Error that get's created:

Tuesday, September 26, 2023: 15:11:54	CMD: touch /scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/partitioned_reads.files.list.ok
Tuesday, September 26, 2023: 15:11:54	CMD: /usr/local/opt/trinity-2.13.2/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  --min_contig_length  200  --NO_SEQTK  --no_salmon  > recursive_trinity.cmds
Error, reads file listing: /scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/partitioned_reads.files.list is empty.  This tends to happen when there were too few reads to assemble.  at /usr/local/opt/trinity-2.13.2/util/support_scripts/write_partitioned_trinity_cmds.pl line 51.
Error, cmd: /usr/local/opt/trinity-2.13.2/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  --min_contig_length  200  --NO_SEQTK  --no_salmon  > recursive_trinity.cmds died with ret 65280 at /usr/local/bin/Trinity line 2863.
	main::process_cmd("/usr/local/opt/trinity-2.13.2/util/support_scripts/write_part"...) called at /usr/local/bin/Trinity line 3672
	main::write_trinity_partitioned_cmds("/scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/"..., "recursive_trinity.cmds", "GENOME-FREE_MODE") called at /usr/local/bin/Trinity line 2456
	main::run_recursive_trinity("/scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/"...) called at /usr/local/bin/Trinity line 2215
	main::run_chrysalis("/scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/"..., "/scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/"..., 200, 500, undef, "/scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/"..., "/scratch/leuven/344/vsc34477/nxf.GZeAyNhvBP/LVE00083_trinity/"...) called at /usr/local/bin/Trinity line 1839
	main::run_Trinity() called at /usr/local/bin/Trinity line 1444
	eval {...} called at /usr/local/bin/Trinity line 1443

Trinity run failed. Must investigate error above.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[Joon-Klaps]

Ignoring the error, results in an output of "Null" this needs to be filtered out first