[2023-06-07 20:40:12,238] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:40:12,240] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:40:12,240] [INFO] DQC Reference Directory: /var/lib/cwl/stge8aeeee7-9f2f-43d6-a1c1-27a1bed5c931/dqc_reference
[2023-06-07 20:40:13,742] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:40:13,743] [INFO] Task started: Prodigal
[2023-06-07 20:40:13,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ba18260-cecd-4094-a6d4-0c5b4e4ec3ef/GCA_902635895.1_AG-447-O05_genomic.fna.gz | prodigal -d GCA_902635895.1_AG-447-O05_genomic.fna/cds.fna -a GCA_902635895.1_AG-447-O05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:40:17,430] [INFO] Task succeeded: Prodigal
[2023-06-07 20:40:17,430] [INFO] Task started: HMMsearch
[2023-06-07 20:40:17,431] [INFO] Running command: hmmsearch --tblout GCA_902635895.1_AG-447-O05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8aeeee7-9f2f-43d6-a1c1-27a1bed5c931/dqc_reference/reference_markers.hmm GCA_902635895.1_AG-447-O05_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:40:17,669] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:40:17,671] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4ba18260-cecd-4094-a6d4-0c5b4e4ec3ef/GCA_902635895.1_AG-447-O05_genomic.fna.gz]
[2023-06-07 20:40:17,691] [INFO] Query marker FASTA was written to GCA_902635895.1_AG-447-O05_genomic.fna/markers.fasta
[2023-06-07 20:40:17,691] [INFO] Task started: Blastn
[2023-06-07 20:40:17,692] [INFO] Running command: blastn -query GCA_902635895.1_AG-447-O05_genomic.fna/markers.fasta -db /var/lib/cwl/stge8aeeee7-9f2f-43d6-a1c1-27a1bed5c931/dqc_reference/reference_markers.fasta -out GCA_902635895.1_AG-447-O05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:18,292] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:18,297] [INFO] Selected 21 target genomes.
[2023-06-07 20:40:18,298] [INFO] Target genome list was writen to GCA_902635895.1_AG-447-O05_genomic.fna/target_genomes.txt
[2023-06-07 20:40:18,308] [INFO] Task started: fastANI
[2023-06-07 20:40:18,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba18260-cecd-4094-a6d4-0c5b4e4ec3ef/GCA_902635895.1_AG-447-O05_genomic.fna.gz --refList GCA_902635895.1_AG-447-O05_genomic.fna/target_genomes.txt --output GCA_902635895.1_AG-447-O05_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:40:30,719] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:30,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8aeeee7-9f2f-43d6-a1c1-27a1bed5c931/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:40:30,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8aeeee7-9f2f-43d6-a1c1-27a1bed5c931/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:40:30,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:40:30,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 20:40:30,721] [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
--------------------------------------------------------------------------------
[2023-06-07 20:40:30,723] [INFO] DFAST Taxonomy check result was written to GCA_902635895.1_AG-447-O05_genomic.fna/tc_result.tsv
[2023-06-07 20:40:30,724] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:40:30,724] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:40:30,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8aeeee7-9f2f-43d6-a1c1-27a1bed5c931/dqc_reference/checkm_data
[2023-06-07 20:40:30,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:40:30,746] [INFO] Task started: CheckM
[2023-06-07 20:40:30,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902635895.1_AG-447-O05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902635895.1_AG-447-O05_genomic.fna/checkm_input GCA_902635895.1_AG-447-O05_genomic.fna/checkm_result
[2023-06-07 20:40:49,386] [INFO] Task succeeded: CheckM
[2023-06-07 20:40:49,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:40:49,401] [INFO] ===== Completeness check finished =====
[2023-06-07 20:40:49,401] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:40:49,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902635895.1_AG-447-O05_genomic.fna/markers.fasta)
[2023-06-07 20:40:49,402] [INFO] Task started: Blastn
[2023-06-07 20:40:49,402] [INFO] Running command: blastn -query GCA_902635895.1_AG-447-O05_genomic.fna/markers.fasta -db /var/lib/cwl/stge8aeeee7-9f2f-43d6-a1c1-27a1bed5c931/dqc_reference/reference_markers_gtdb.fasta -out GCA_902635895.1_AG-447-O05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:50,212] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:50,215] [INFO] Selected 12 target genomes.
[2023-06-07 20:40:50,216] [INFO] Target genome list was writen to GCA_902635895.1_AG-447-O05_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:40:50,225] [INFO] Task started: fastANI
[2023-06-07 20:40:50,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba18260-cecd-4094-a6d4-0c5b4e4ec3ef/GCA_902635895.1_AG-447-O05_genomic.fna.gz --refList GCA_902635895.1_AG-447-O05_genomic.fna/target_genomes_gtdb.txt --output GCA_902635895.1_AG-447-O05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:40:54,043] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:54,059] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:40:54,059] [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
GCA_902635895.1	s__MAG-121220-bin8 sp902635895	100.0	409	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.57	96.57	0.70	0.70	2	conclusive
GCA_016780345.1	s__MAG-121220-bin8 sp016780345	87.7983	280	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.67	99.67	0.79	0.79	2	-
GCA_004214185.1	s__MAG-121220-bin8 sp004214185	80.8072	214	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	80.2482	244	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_902510655.1	s__MAG-121220-bin8 sp902510655	79.0893	145	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	78.5097	188	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	78.39	166	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	78.0795	150	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	77.9059	135	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	77.7716	148	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	77.5538	112	412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
--------------------------------------------------------------------------------
[2023-06-07 20:40:54,061] [INFO] GTDB search result was written to GCA_902635895.1_AG-447-O05_genomic.fna/result_gtdb.tsv
[2023-06-07 20:40:54,062] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:40:54,067] [INFO] DFAST_QC result json was written to GCA_902635895.1_AG-447-O05_genomic.fna/dqc_result.json
[2023-06-07 20:40:54,067] [INFO] DFAST_QC completed!
[2023-06-07 20:40:54,068] [INFO] Total running time: 0h0m42s