[2024-01-24 12:14:35,250] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,255] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,256] [INFO] DQC Reference Directory: /var/lib/cwl/stg2463eddd-c926-4e19-a416-157efcba8843/dqc_reference
[2024-01-24 12:14:36,543] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,544] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg1483e773-3dc0-4c15-8a29-b4555a4b630a/GCF_000438785.2_ASM43878v2_genomic.fna.gz | prodigal -d GCF_000438785.2_ASM43878v2_genomic.fna/cds.fna -a GCF_000438785.2_ASM43878v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:48,685] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:48,686] [INFO] Task started: HMMsearch
[2024-01-24 12:14:48,686] [INFO] Running command: hmmsearch --tblout GCF_000438785.2_ASM43878v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2463eddd-c926-4e19-a416-157efcba8843/dqc_reference/reference_markers.hmm GCF_000438785.2_ASM43878v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:49,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:49,015] [INFO] Found 6/6 markers.
[2024-01-24 12:14:49,063] [INFO] Query marker FASTA was written to GCF_000438785.2_ASM43878v2_genomic.fna/markers.fasta
[2024-01-24 12:14:49,064] [INFO] Task started: Blastn
[2024-01-24 12:14:49,064] [INFO] Running command: blastn -query GCF_000438785.2_ASM43878v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2463eddd-c926-4e19-a416-157efcba8843/dqc_reference/reference_markers.fasta -out GCF_000438785.2_ASM43878v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:49,966] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:49,970] [INFO] Selected 9 target genomes.
[2024-01-24 12:14:49,970] [INFO] Target genome list was writen to GCF_000438785.2_ASM43878v2_genomic.fna/target_genomes.txt
[2024-01-24 12:14:49,975] [INFO] Task started: fastANI
[2024-01-24 12:14:49,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg1483e773-3dc0-4c15-8a29-b4555a4b630a/GCF_000438785.2_ASM43878v2_genomic.fna.gz --refList GCF_000438785.2_ASM43878v2_genomic.fna/target_genomes.txt --output GCF_000438785.2_ASM43878v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:59,922] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:59,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2463eddd-c926-4e19-a416-157efcba8843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:59,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2463eddd-c926-4e19-a416-157efcba8843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:59,932] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:14:59,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:59,933] [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 natriegens	strain=DSM 759	GCA_000438785.2	691	691	type	True	100.0	1612	1621	95	conclusive
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	99.99	1620	1621	95	conclusive
Vibrio natriegens	strain=ATCC 14048	GCA_001680025.1	691	691	type	True	99.987	1616	1621	95	conclusive
Vibrio natriegens	strain=NBRC 15636	GCA_001591085.1	691	691	type	True	99.9851	1609	1621	95	conclusive
Vibrio natriegens	strain=ATCC 14048	GCA_000417905.1	691	691	type	True	99.9814	1606	1621	95	conclusive
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.0884	348	1621	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.0429	350	1621	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.6621	432	1621	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.6409	430	1621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:59,935] [INFO] DFAST Taxonomy check result was written to GCF_000438785.2_ASM43878v2_genomic.fna/tc_result.tsv
[2024-01-24 12:14:59,935] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:59,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:59,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2463eddd-c926-4e19-a416-157efcba8843/dqc_reference/checkm_data
[2024-01-24 12:14:59,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:59,992] [INFO] Task started: CheckM
[2024-01-24 12:14:59,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000438785.2_ASM43878v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000438785.2_ASM43878v2_genomic.fna/checkm_input GCF_000438785.2_ASM43878v2_genomic.fna/checkm_result
[2024-01-24 12:15:40,722] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:40,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:40,749] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:40,749] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:40,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000438785.2_ASM43878v2_genomic.fna/markers.fasta)
[2024-01-24 12:15:40,750] [INFO] Task started: Blastn
[2024-01-24 12:15:40,750] [INFO] Running command: blastn -query GCF_000438785.2_ASM43878v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2463eddd-c926-4e19-a416-157efcba8843/dqc_reference/reference_markers_gtdb.fasta -out GCF_000438785.2_ASM43878v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:41,957] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:41,965] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:41,966] [INFO] Target genome list was writen to GCF_000438785.2_ASM43878v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:41,973] [INFO] Task started: fastANI
[2024-01-24 12:15:41,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg1483e773-3dc0-4c15-8a29-b4555a4b630a/GCF_000438785.2_ASM43878v2_genomic.fna.gz --refList GCF_000438785.2_ASM43878v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000438785.2_ASM43878v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:51,716] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:51,728] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:51,728] [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_000417905.1	s__Vibrio natriegens	99.9814	1606	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	conclusive
GCA_018223135.1	s__Vibrio sp018223135	91.5233	1167	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222805.1	s__Vibrio sp018222805	90.0377	1157	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905175385.1	s__Vibrio sp903986855	83.6156	1001	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.95	0.95	0.92	4	-
GCF_900460535.1	s__Vibrio parahaemolyticus	83.2584	906	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCA_001048675.1	s__Vibrio diabolicus	83.0341	864	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_000354175.2	s__Vibrio alginolyticus	82.7846	861	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_002741985.1	s__Vibrio rotiferianus	82.0272	751	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000830505.1	s__Vibrio mytili	81.8274	750	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:51,730] [INFO] GTDB search result was written to GCF_000438785.2_ASM43878v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:51,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:51,733] [INFO] DFAST_QC result json was written to GCF_000438785.2_ASM43878v2_genomic.fna/dqc_result.json
[2024-01-24 12:15:51,733] [INFO] DFAST_QC completed!
[2024-01-24 12:15:51,733] [INFO] Total running time: 0h1m16s