Is the orientation parameter necessary when running metaviral with illumina PE RNASeq datasets?

[grendon]

Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above.

The input is RNASeq Illumina PE. Read1 aligns to the ANTISENSE strand and Read2 aligns to the SENSE strand. We want as output a viral meta-transcriptome assembly; so I wonder which command is correct, with or without orientation parameter? If we need to specify orientation, how can it be done at the command line without a YAML file?

cmd1:

spades.py -o ./output_w_rnaviral  --tmp-dir /scratch/grendon/spades/  --rnaviral  -t 24 -m 50 -1 H170_1.fq -2 H170_2.fq 

cmd2:

spades.py -o ./output_w_rnaviral_w_yaml  --tmp-dir /scratch/grendon/spades/  --rnaviral  -t 24 -m 50 --dataset input_dataset.yaml

Where input_dataset.yaml is:

- "left reads":
  - "/some/path/H170_1.fq"
  "number": !!int "1"
  "orientation": "rf"
  "right reads":
  - "/some/path/H170_2.fq"
  "type": "paired-end"

The second command generated this warning:

=== Error correction and assembling warnings:
 * 0:00:09.247    83M / 12G   WARN    General                 (pair_info_count.cpp       : 377)   Estimated mean insert size 99.007 is very small compared to read length 150
======= Warnings saved to /some/path/output_w_rnaviral_w_yaml/warnings.log

Describe the solution you'd like

No response

Describe alternatives you've considered

No response

Additional context

No response