[2023-03-18 03:09:33,543] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,543] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,543] [INFO] DQC Reference Directory: /var/lib/cwl/stgc88904e6-05cf-41ef-b6d5-516f3c8d626d/dqc_reference
[2023-03-18 03:09:34,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,689] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,689] [INFO] Running command: cat /var/lib/cwl/stg10eb2fb1-1c88-4afc-80e6-91505f148cb3/OceanDNA-b26766.fa | prodigal -d OceanDNA-b26766/cds.fna -a OceanDNA-b26766/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:43,859] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:43,859] [INFO] Task started: HMMsearch
[2023-03-18 03:09:43,859] [INFO] Running command: hmmsearch --tblout OceanDNA-b26766/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc88904e6-05cf-41ef-b6d5-516f3c8d626d/dqc_reference/reference_markers.hmm OceanDNA-b26766/protein.faa > /dev/null
[2023-03-18 03:09:44,074] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:44,075] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg10eb2fb1-1c88-4afc-80e6-91505f148cb3/OceanDNA-b26766.fa]
[2023-03-18 03:09:44,091] [INFO] Query marker FASTA was written to OceanDNA-b26766/markers.fasta
[2023-03-18 03:09:44,091] [INFO] Task started: Blastn
[2023-03-18 03:09:44,091] [INFO] Running command: blastn -query OceanDNA-b26766/markers.fasta -db /var/lib/cwl/stgc88904e6-05cf-41ef-b6d5-516f3c8d626d/dqc_reference/reference_markers.fasta -out OceanDNA-b26766/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:44,710] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:44,711] [INFO] Selected 29 target genomes.
[2023-03-18 03:09:44,711] [INFO] Target genome list was writen to OceanDNA-b26766/target_genomes.txt
[2023-03-18 03:09:44,726] [INFO] Task started: fastANI
[2023-03-18 03:09:44,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg10eb2fb1-1c88-4afc-80e6-91505f148cb3/OceanDNA-b26766.fa --refList OceanDNA-b26766/target_genomes.txt --output OceanDNA-b26766/fastani_result.tsv --threads 1
[2023-03-18 03:10:04,921] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:04,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc88904e6-05cf-41ef-b6d5-516f3c8d626d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:04,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc88904e6-05cf-41ef-b6d5-516f3c8d626d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:04,925] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:10:04,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:10:04,925] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	75.7277	50	379	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:04,925] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26766/tc_result.tsv
[2023-03-18 03:10:04,925] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:04,925] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:04,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc88904e6-05cf-41ef-b6d5-516f3c8d626d/dqc_reference/checkm_data
[2023-03-18 03:10:04,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:04,939] [INFO] Task started: CheckM
[2023-03-18 03:10:04,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26766/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26766/checkm_input OceanDNA-b26766/checkm_result
[2023-03-18 03:10:33,058] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:33,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.38%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:33,061] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:33,061] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:33,061] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26766/markers.fasta)
[2023-03-18 03:10:33,061] [INFO] Task started: Blastn
[2023-03-18 03:10:33,062] [INFO] Running command: blastn -query OceanDNA-b26766/markers.fasta -db /var/lib/cwl/stgc88904e6-05cf-41ef-b6d5-516f3c8d626d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26766/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:34,089] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:34,090] [INFO] Selected 29 target genomes.
[2023-03-18 03:10:34,090] [INFO] Target genome list was writen to OceanDNA-b26766/target_genomes_gtdb.txt
[2023-03-18 03:10:34,196] [INFO] Task started: fastANI
[2023-03-18 03:10:34,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg10eb2fb1-1c88-4afc-80e6-91505f148cb3/OceanDNA-b26766.fa --refList OceanDNA-b26766/target_genomes_gtdb.txt --output OceanDNA-b26766/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:10:58,196] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:58,200] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:10:58,200] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000179775.1	s__R2A130 sp000179775	76.2259	77	379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	75.7277	50	379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002295065.1	s__Mesorhizobium sp002295065	75.7199	51	379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791585.1	s__Mesorhizobium sp004791585	75.4614	60	379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
--------------------------------------------------------------------------------
[2023-03-18 03:10:58,200] [INFO] GTDB search result was written to OceanDNA-b26766/result_gtdb.tsv
[2023-03-18 03:10:58,200] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:10:58,201] [INFO] DFAST_QC result json was written to OceanDNA-b26766/dqc_result.json
[2023-03-18 03:10:58,201] [INFO] DFAST_QC completed!
[2023-03-18 03:10:58,201] [INFO] Total running time: 0h1m25s