[2024-01-24 11:09:50,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,797] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1156a1b-7dcb-4cda-8612-e46f44cbe17a/dqc_reference
[2024-01-24 11:09:53,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,304] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,304] [INFO] Running command: gunzip -c /var/lib/cwl/stgd82360d9-5d42-4bb9-9a99-a10e54c939db/GCF_022869905.1_ASM2286990v1_genomic.fna.gz | prodigal -d GCF_022869905.1_ASM2286990v1_genomic.fna/cds.fna -a GCF_022869905.1_ASM2286990v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:09,028] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:09,028] [INFO] Task started: HMMsearch
[2024-01-24 11:10:09,029] [INFO] Running command: hmmsearch --tblout GCF_022869905.1_ASM2286990v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1156a1b-7dcb-4cda-8612-e46f44cbe17a/dqc_reference/reference_markers.hmm GCF_022869905.1_ASM2286990v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:09,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:09,318] [INFO] Found 6/6 markers.
[2024-01-24 11:10:09,360] [INFO] Query marker FASTA was written to GCF_022869905.1_ASM2286990v1_genomic.fna/markers.fasta
[2024-01-24 11:10:09,360] [INFO] Task started: Blastn
[2024-01-24 11:10:09,360] [INFO] Running command: blastn -query GCF_022869905.1_ASM2286990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1156a1b-7dcb-4cda-8612-e46f44cbe17a/dqc_reference/reference_markers.fasta -out GCF_022869905.1_ASM2286990v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:10,207] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:10,210] [INFO] Selected 9 target genomes.
[2024-01-24 11:10:10,211] [INFO] Target genome list was writen to GCF_022869905.1_ASM2286990v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:10,218] [INFO] Task started: fastANI
[2024-01-24 11:10:10,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgd82360d9-5d42-4bb9-9a99-a10e54c939db/GCF_022869905.1_ASM2286990v1_genomic.fna.gz --refList GCF_022869905.1_ASM2286990v1_genomic.fna/target_genomes.txt --output GCF_022869905.1_ASM2286990v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:20,433] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:20,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1156a1b-7dcb-4cda-8612-e46f44cbe17a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:20,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1156a1b-7dcb-4cda-8612-e46f44cbe17a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:20,447] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:10:20,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:20,448] [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
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	100.0	1662	1663	95	conclusive
Vibrio furnissii	strain=NCTC13120	GCA_900460225.1	29494	29494	type	True	99.9996	1660	1663	95	conclusive
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	99.9989	1660	1663	95	conclusive
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	99.9946	1634	1663	95	conclusive
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	87.6575	1301	1663	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	80.0572	546	1663	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.595	416	1663	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.5273	343	1663	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	79.0182	374	1663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:20,449] [INFO] DFAST Taxonomy check result was written to GCF_022869905.1_ASM2286990v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:20,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:20,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:20,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1156a1b-7dcb-4cda-8612-e46f44cbe17a/dqc_reference/checkm_data
[2024-01-24 11:10:20,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:20,512] [INFO] Task started: CheckM
[2024-01-24 11:10:20,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022869905.1_ASM2286990v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022869905.1_ASM2286990v1_genomic.fna/checkm_input GCF_022869905.1_ASM2286990v1_genomic.fna/checkm_result
[2024-01-24 11:11:08,651] [INFO] Task succeeded: CheckM
[2024-01-24 11:11:08,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:11:08,679] [INFO] ===== Completeness check finished =====
[2024-01-24 11:11:08,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:11:08,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022869905.1_ASM2286990v1_genomic.fna/markers.fasta)
[2024-01-24 11:11:08,680] [INFO] Task started: Blastn
[2024-01-24 11:11:08,681] [INFO] Running command: blastn -query GCF_022869905.1_ASM2286990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1156a1b-7dcb-4cda-8612-e46f44cbe17a/dqc_reference/reference_markers_gtdb.fasta -out GCF_022869905.1_ASM2286990v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:11:10,019] [INFO] Task succeeded: Blastn
[2024-01-24 11:11:10,024] [INFO] Selected 17 target genomes.
[2024-01-24 11:11:10,024] [INFO] Target genome list was writen to GCF_022869905.1_ASM2286990v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:11:10,080] [INFO] Task started: fastANI
[2024-01-24 11:11:10,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgd82360d9-5d42-4bb9-9a99-a10e54c939db/GCF_022869905.1_ASM2286990v1_genomic.fna.gz --refList GCF_022869905.1_ASM2286990v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022869905.1_ASM2286990v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:11:26,211] [INFO] Task succeeded: fastANI
[2024-01-24 11:11:26,228] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:11:26,229] [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_000176175.1	s__Vibrio furnissii	99.9946	1634	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	conclusive
GCF_900460245.1	s__Vibrio fluvialis	87.6546	1311	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_019226825.1	s__Vibrio sp004804295	81.5188	796	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.23	99.23	0.93	0.93	2	-
GCF_019048845.1	s__Vibrio sp000176715	80.2067	508	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.20	96.20	0.92	0.92	2	-
GCF_009763805.1	s__Vibrio cidicii	80.0758	467	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.20	97.77	0.90	0.87	8	-
GCF_001471585.2	s__Vibrio cholerae	80.0101	526	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.72	95.09	0.90	0.82	1544	-
GCF_000764325.1	s__Vibrio navarrensis	79.9902	478	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCF_009665255.1	s__Vibrio metoecus_B	79.9485	520	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCA_015767675.1	s__Vibrio sp000960595	79.8147	470	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.38	0.94	0.90	8	-
GCF_011064285.1	s__Vibrio ziniensis	79.8058	478	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460535.1	s__Vibrio parahaemolyticus	79.5965	439	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCF_900167345.1	s__Vibrio cincinnatiensis	79.5751	402	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	99.06	0.97	0.94	6	-
GCF_009938205.1	s__Vibrio panuliri	79.5283	343	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_000467125.1	s__Vibrio proteolyticus	79.4865	493	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.93	98.89	0.93	0.91	5	-
GCF_000696385.1	s__Vibrio metoecus	79.2864	514	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.79	97.58	0.93	0.89	26	-
GCF_002749895.1	s__Vibrio fujianensis	79.2087	357	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.21	99.14	0.95	0.93	8	-
GCF_000417905.1	s__Vibrio natriegens	79.0471	386	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 11:11:26,231] [INFO] GTDB search result was written to GCF_022869905.1_ASM2286990v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:11:26,232] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:11:26,236] [INFO] DFAST_QC result json was written to GCF_022869905.1_ASM2286990v1_genomic.fna/dqc_result.json
[2024-01-24 11:11:26,237] [INFO] DFAST_QC completed!
[2024-01-24 11:11:26,237] [INFO] Total running time: 0h1m36s