[2023-06-30 07:43:29,611] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:43:29,613] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:43:29,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7f6875a-3b98-4271-8b30-073145f0cc4f/dqc_reference
[2023-06-30 07:43:30,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:43:30,866] [INFO] Task started: Prodigal
[2023-06-30 07:43:30,866] [INFO] Running command: gunzip -c /var/lib/cwl/stg0396cb56-66f0-45bd-aab9-cadc9725a31a/GCA_016708985.1_ASM1670898v1_genomic.fna.gz | prodigal -d GCA_016708985.1_ASM1670898v1_genomic.fna/cds.fna -a GCA_016708985.1_ASM1670898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:43:58,938] [INFO] Task succeeded: Prodigal
[2023-06-30 07:43:58,938] [INFO] Task started: HMMsearch
[2023-06-30 07:43:58,938] [INFO] Running command: hmmsearch --tblout GCA_016708985.1_ASM1670898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7f6875a-3b98-4271-8b30-073145f0cc4f/dqc_reference/reference_markers.hmm GCA_016708985.1_ASM1670898v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:43:59,225] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:43:59,226] [INFO] Found 6/6 markers.
[2023-06-30 07:43:59,268] [INFO] Query marker FASTA was written to GCA_016708985.1_ASM1670898v1_genomic.fna/markers.fasta
[2023-06-30 07:43:59,268] [INFO] Task started: Blastn
[2023-06-30 07:43:59,268] [INFO] Running command: blastn -query GCA_016708985.1_ASM1670898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7f6875a-3b98-4271-8b30-073145f0cc4f/dqc_reference/reference_markers.fasta -out GCA_016708985.1_ASM1670898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:43:59,862] [INFO] Task succeeded: Blastn
[2023-06-30 07:43:59,866] [INFO] Selected 24 target genomes.
[2023-06-30 07:43:59,867] [INFO] Target genome list was writen to GCA_016708985.1_ASM1670898v1_genomic.fna/target_genomes.txt
[2023-06-30 07:43:59,872] [INFO] Task started: fastANI
[2023-06-30 07:43:59,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg0396cb56-66f0-45bd-aab9-cadc9725a31a/GCA_016708985.1_ASM1670898v1_genomic.fna.gz --refList GCA_016708985.1_ASM1670898v1_genomic.fna/target_genomes.txt --output GCA_016708985.1_ASM1670898v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:44:14,225] [INFO] Task succeeded: fastANI
[2023-06-30 07:44:14,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7f6875a-3b98-4271-8b30-073145f0cc4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:44:14,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7f6875a-3b98-4271-8b30-073145f0cc4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:44:14,229] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:44:14,229] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 07:44:14,230] [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
--------------------------------------------------------------------------------
[2023-06-30 07:44:14,232] [INFO] DFAST Taxonomy check result was written to GCA_016708985.1_ASM1670898v1_genomic.fna/tc_result.tsv
[2023-06-30 07:44:14,233] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:44:14,233] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:44:14,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7f6875a-3b98-4271-8b30-073145f0cc4f/dqc_reference/checkm_data
[2023-06-30 07:44:14,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:44:14,286] [INFO] Task started: CheckM
[2023-06-30 07:44:14,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708985.1_ASM1670898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708985.1_ASM1670898v1_genomic.fna/checkm_input GCA_016708985.1_ASM1670898v1_genomic.fna/checkm_result
[2023-06-30 07:45:34,505] [INFO] Task succeeded: CheckM
[2023-06-30 07:45:34,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 07:45:34,527] [INFO] ===== Completeness check finished =====
[2023-06-30 07:45:34,527] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:45:34,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708985.1_ASM1670898v1_genomic.fna/markers.fasta)
[2023-06-30 07:45:34,528] [INFO] Task started: Blastn
[2023-06-30 07:45:34,528] [INFO] Running command: blastn -query GCA_016708985.1_ASM1670898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7f6875a-3b98-4271-8b30-073145f0cc4f/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708985.1_ASM1670898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:45:35,281] [INFO] Task succeeded: Blastn
[2023-06-30 07:45:35,286] [INFO] Selected 21 target genomes.
[2023-06-30 07:45:35,286] [INFO] Target genome list was writen to GCA_016708985.1_ASM1670898v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:45:35,298] [INFO] Task started: fastANI
[2023-06-30 07:45:35,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg0396cb56-66f0-45bd-aab9-cadc9725a31a/GCA_016708985.1_ASM1670898v1_genomic.fna.gz --refList GCA_016708985.1_ASM1670898v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708985.1_ASM1670898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:45:48,507] [INFO] Task succeeded: fastANI
[2023-06-30 07:45:48,533] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:45:48,533] [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_016704485.1	s__PHOS-HE28 sp016704485	99.5864	1384	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.65	99.54	0.98	0.96	6	conclusive
GCA_017987115.1	s__PHOS-HE28 sp017987115	85.0614	910	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705955.1	s__PHOS-HE28 sp016705955	78.1813	170	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717305.1	s__PHOS-HE28 sp016717305	77.8976	241	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.11	99.05	0.96	0.96	3	-
GCA_016710015.1	s__PHOS-HE28 sp016710015	77.5929	204	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.59	99.44	0.96	0.92	12	-
GCA_016718655.1	s__PHOS-HE28 sp016718655	77.4725	134	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	98.66	98.64	0.87	0.86	3	-
GCA_014584605.1	s__PHOS-HE28 sp014584605	77.2449	59	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267065.1	s__PHOS-HE28 sp018267065	76.9453	62	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826215.1	s__PHOS-HE28 sp902826215	76.9085	198	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717225.1	s__PHOS-HE28 sp016717225	76.8655	115	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	98.49	98.49	0.88	0.88	2	-
GCA_016788205.1	s__PHOS-HE28 sp016788205	76.8402	147	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360495.1	s__PHOS-HE28 sp002360495	76.735	131	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	97.35	97.35	0.85	0.85	2	-
GCA_018266685.1	s__PHOS-HE28 sp018266685	76.6595	81	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.70	99.70	0.93	0.93	2	-
GCA_018057455.1	s__PHOS-HE28 sp018057455	76.6176	80	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.80	99.80	0.93	0.93	2	-
GCA_016713865.1	s__PHOS-HE28 sp016713865	76.5541	94	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787995.1	s__PHOS-HE28 sp016787995	76.4675	96	1429	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 07:45:48,535] [INFO] GTDB search result was written to GCA_016708985.1_ASM1670898v1_genomic.fna/result_gtdb.tsv
[2023-06-30 07:45:48,536] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:45:48,539] [INFO] DFAST_QC result json was written to GCA_016708985.1_ASM1670898v1_genomic.fna/dqc_result.json
[2023-06-30 07:45:48,539] [INFO] DFAST_QC completed!
[2023-06-30 07:45:48,539] [INFO] Total running time: 0h2m19s