Humann in two steps


I tried to run biobakery workflows and it worked with kneadData and MetaPhlAn. HUMAnN gave me an error inside workflows, so I tried to run the program separately.

When I used MetaPhlAn sam and tsv files I received all UNMAPED.

humann --input EC1_bowtie2.sam --taxonomic-profile EC1_taxonomic_profile.tsv --output /media/microviable/e/EC1/humann --threads 4 --o-log /media/microviable/e/EC1/humann/EC1.log
Creating output directory: /media/microviable/e/EC1/humann
Output files will be written to: /media/microviable/e/EC1/humann
Process the sam mapping results …
Computing gene families …
Computing pathways abundance and coverage …
Output files created:

When I use kneadData fastq, I received another error

humann --input EC1.fastq --output /media/microviable/e/EC1/humann --threads 4 --o-log /media/microviable/e/EC1/humann/EC1.log
Output files will be written to: /media/microviable/e/EC1/humann
Running metaphlan …
Found g__Lachnospiraceae_unclassified.s__Eubacterium_rectale : 34.83% of mapped reads

Total species selected from prescreen: 71
Selected species explain 99.94% of predicted community composition
Creating custom ChocoPhlAn database …
Running bowtie2-build …
Running bowtie2 …
Total bugs from nucleotide alignment: 71
g__Roseburia.s__Roseburia_intestinalis: 81376 hits

Total gene families from nucleotide alignment: 145662
Unaligned reads after nucleotide alignment: 45.3554444501 %
Running diamond …
Aligning to reference database: uniref90_201901b_full.dmnd
CRITICAL ERROR: Error executing: /home/microviable/miniconda3/envs/humann3/bin/diamond blastx --query /media/microviable/e/EC1/humann/EC1_humann_temp/EC1_bowtie2_unaligned.fa --evalue 1.0 --threads 4 --top 1 --outfmt 6 --db /media/microviable/e/biobakery_workflows_databases/humann/uniref/uniref90_201901b_full --out /media/microviable/e/EC1/humann/EC1_humann_temp/tmpo2hu4iuj/diamond_m8_4nfyskk2 --tmpdir /media/microviable/e/EC1/humann/EC1_humann_temp/tmpo2hu4iuj
Error message returned from diamond :
diamond v0.9.36.137 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at
#CPU threads: 4
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /media/microviable/e/EC1/humann/EC1_humann_temp/tmpo2hu4iuj
Opening the database… [0.562s]
Percentage range of top alignment score to report hits: 1
Reference = /media/microviable/e/biobakery_workflows_databases/humann/uniref/uniref90_201901b_full.dmnd
Sequences = 87296736
Letters = 29247941583
Block size = 2000000000
Opening the input file… [0.33s]
Opening the output file… [0.001s]
Loading query sequences… [16.939s]
Masking queries… [23.073s]
Building query seed set… [0.057s]
Algorithm: Double-indexed
Building query histograms… [6.458s]
Allocating buffers… [0s]
Loading reference sequences… [0s]
Error: Unexpected end of input.

So I tried to use sam and tsv files from this process and it worked.

I don’t know what is the problem.

Any help?