low number of reads detected

[rzhan186]

Hi Dr. Woodcroft,

I am currently utilizing graftM to analyze the community profiles of methane-cycling microbes within my assembled contigs, employing the mcrA, pmoA, and mmoX graftM packages. In my workflow, I attempted to utilize translated sequences as input for graftM. However, upon observation, despite the input file size being approximately 2.1 GB and containing millions of sequences, when applying the mcrA package to the translated contigs, graftM reported only "35 read(s) detected."

While the software completed the execution successfully, I suspect this might not be the correct behavior due to the low number of reads detected.

I am seeking assistance to troubleshoot and identify the possible reasons.

For your reference, I am using graftM version 0.15 within a Docker container. Below are the inputs and outputs of my analysis:

apptainer run -C -B /project -B /scratch $SCRATCH/graftm-0.15.0.sif \
graft --forward $input/proteins.faa \
--graftm_package $gpkg/7.27.methyl_coenzyme_reductase_alpha_subunit.mcrA.gpkg \
--output_directory test \

Here are the outputs:

02/29/2024 04:33:40 PM INFO: Working on gy2021_SK_sur_t6_proteins
02/29/2024 04:34:25 PM INFO: 35 read(s) detected
02/29/2024 04:34:25 PM INFO: aligning reads to reference package database
02/29/2024 04:34:25 PM INFO: Filtered 0 short sequences from the alignment
02/29/2024 04:34:25 PM INFO: 35 sequences remaining
02/29/2024 04:34:25 PM INFO: Placing reads into phylogenetic tree
02/29/2024 04:34:32 PM INFO: Placements finished
02/29/2024 04:34:32 PM INFO: Reading classifications
02/29/2024 04:34:32 PM INFO: Reads classified
02/29/2024 04:34:32 PM INFO: Writing summary table
02/29/2024 04:34:32 PM INFO: Writing biom file
02/29/2024 04:34:32 PM INFO: Building summary krona plot
02/29/2024 04:34:33 PM INFO: Cleaning up
02/29/2024 04:34:33 PM INFO: Done, thanks for using graftM!

Thank you!