sushilab / mtags Goto Github PK

Hi,
Thanks for the developing of the taxonomic profiling tool.
in my case, the mitag download failed several times. Are there other ways to complete this step?
Looking forward for your reply.

Hello,
can MTAGs be used with metatranscriptomic data?
When I tried, I got the following message:
2023-03-10 17:29:08,695 ERROR: Command hmmsearch --cpu 4 -o mtags/clean_21_1_R1_qual.fastq_fw.fasta_ssu.hmmer --domtblout mtags/clean_21_1_R1_qual.fastq_fw.fasta_ssu.dom -E 0.01 /projects/lavi3948/software/anaconda/envs/mtags/lib/python3.7/site-packages/mTAGs/data/ssu.hmm mtags/clean_21_1_R1_qual.fastq_fw.fasta failed with message: None
2023-03-10 17:29:08,696 INFO: mTAGs finished with error code 1

Steps:

1. install mTags via conda
2. download mTags database
3. run profile

Error message:
2024-02-24 17:35:26,237 INFO: Processed reads: 36000000
Traceback (most recent call last):
File "/Applications/miniconda3/envs/mtags/bin/mtags", line 8, in
sys.exit(main())
File "/Applications/miniconda3/envs/mtags/lib/python3.7/site-packages/mTAGs/mtags.py", line 1284, in main
execute_mtags_profile(sys.argv[2:])
File "/Applications/miniconda3/envs/mtags/lib/python3.7/site-packages/mTAGs/mtags.py", line 1219, in execute_mtags_profile
ssu_files = _mtags_extract_grouped(input_seqfiles_r1, input_seqfiles_r2, input_seqfiles_s, output_folder, threads)
File "/Applications/miniconda3/envs/mtags/lib/python3.7/site-packages/mTAGs/mtags.py", line 536, in _mtags_extract_grouped
(reads_s, ssu_files_s, lsu_file_s) = mtags_extract(pathlib.Path(input_seqfile_s), output_folder, readnames, threads=threads)
File "/Applications/miniconda3/envs/mtags/lib/python3.7/site-packages/mTAGs/mtags.py", line 375, in mtags_extract
for number_of_sequences, fasta in enumerate(stream_fa(input_seq_file), 1):
File "/Applications/miniconda3/envs/mtags/lib/python3.7/site-packages/mTAGs/mtags.py", line 162, in stream_fa
for header, sequence, qual in Bio.SeqIO.QualityIO.FastqGeneralIterator(handle):
File "/Applications/miniconda3/envs/mtags/lib/python3.7/site-packages/Bio/SeqIO/QualityIO.py", line 955, in FastqGeneralIterator
raise ValueError("Whitespace is not allowed in the sequence.")
ValueError: Whitespace is not allowed in the sequence.

This is the exact command I used:
% mtags profile -s /Volumes/CanalData2021/METAGENOME.fastq.gz -t 16 -o /Volumes/CanalData2021/test-run-one -n Metagenome_1_Mcd

Note: 2 duplicate fasta files, F and R were generated in the output folder
Note: Metagenomic filtered raw fastq was downloaded from JGI IMG