[2024-01-25 18:15:50,883] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:50,884] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:50,884] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d977f49-c604-4a63-946a-e3beb17b3b27/dqc_reference
[2024-01-25 18:15:52,032] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:52,032] [INFO] Task started: Prodigal
[2024-01-25 18:15:52,033] [INFO] Running command: gunzip -c /var/lib/cwl/stg06c0565e-cfee-49f7-b921-0dae3ef3ddfe/GCF_014050145.1_ASM1405014v1_genomic.fna.gz | prodigal -d GCF_014050145.1_ASM1405014v1_genomic.fna/cds.fna -a GCF_014050145.1_ASM1405014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:01,543] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:01,544] [INFO] Task started: HMMsearch
[2024-01-25 18:16:01,544] [INFO] Running command: hmmsearch --tblout GCF_014050145.1_ASM1405014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d977f49-c604-4a63-946a-e3beb17b3b27/dqc_reference/reference_markers.hmm GCF_014050145.1_ASM1405014v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:01,786] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:01,787] [INFO] Found 6/6 markers.
[2024-01-25 18:16:01,825] [INFO] Query marker FASTA was written to GCF_014050145.1_ASM1405014v1_genomic.fna/markers.fasta
[2024-01-25 18:16:01,825] [INFO] Task started: Blastn
[2024-01-25 18:16:01,825] [INFO] Running command: blastn -query GCF_014050145.1_ASM1405014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d977f49-c604-4a63-946a-e3beb17b3b27/dqc_reference/reference_markers.fasta -out GCF_014050145.1_ASM1405014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:02,576] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:02,578] [INFO] Selected 12 target genomes.
[2024-01-25 18:16:02,579] [INFO] Target genome list was writen to GCF_014050145.1_ASM1405014v1_genomic.fna/target_genomes.txt
[2024-01-25 18:16:02,587] [INFO] Task started: fastANI
[2024-01-25 18:16:02,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c0565e-cfee-49f7-b921-0dae3ef3ddfe/GCF_014050145.1_ASM1405014v1_genomic.fna.gz --refList GCF_014050145.1_ASM1405014v1_genomic.fna/target_genomes.txt --output GCF_014050145.1_ASM1405014v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:13,594] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:13,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d977f49-c604-4a63-946a-e3beb17b3b27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:13,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d977f49-c604-4a63-946a-e3beb17b3b27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:13,603] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:13,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:13,603] [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 marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	100.0	1460	1462	95	conclusive
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	82.2024	807	1462	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	82.1952	813	1462	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	81.6101	781	1462	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	81.5604	801	1462	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	81.1533	617	1462	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	81.0866	655	1462	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	80.6996	608	1462	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	79.7635	467	1462	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.7022	369	1462	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.5747	356	1462	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.4934	351	1462	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:13,604] [INFO] DFAST Taxonomy check result was written to GCF_014050145.1_ASM1405014v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:13,605] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:13,605] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:13,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d977f49-c604-4a63-946a-e3beb17b3b27/dqc_reference/checkm_data
[2024-01-25 18:16:13,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:13,652] [INFO] Task started: CheckM
[2024-01-25 18:16:13,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014050145.1_ASM1405014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014050145.1_ASM1405014v1_genomic.fna/checkm_input GCF_014050145.1_ASM1405014v1_genomic.fna/checkm_result
[2024-01-25 18:16:45,321] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:45,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.76%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:45,344] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:45,344] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:45,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014050145.1_ASM1405014v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:45,345] [INFO] Task started: Blastn
[2024-01-25 18:16:45,345] [INFO] Running command: blastn -query GCF_014050145.1_ASM1405014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d977f49-c604-4a63-946a-e3beb17b3b27/dqc_reference/reference_markers_gtdb.fasta -out GCF_014050145.1_ASM1405014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:46,495] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:46,497] [INFO] Selected 9 target genomes.
[2024-01-25 18:16:46,498] [INFO] Target genome list was writen to GCF_014050145.1_ASM1405014v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:46,500] [INFO] Task started: fastANI
[2024-01-25 18:16:46,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c0565e-cfee-49f7-b921-0dae3ef3ddfe/GCF_014050145.1_ASM1405014v1_genomic.fna.gz --refList GCF_014050145.1_ASM1405014v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014050145.1_ASM1405014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:55,759] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:55,773] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:55,773] [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_014050145.1	s__Vibrio marinisediminis	100.0	1460	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003350325.1	s__Vibrio rhodolitus	82.1952	813	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_009938225.1	s__Vibrio ponticus	82.1938	806	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_015278125.1	s__Vibrio sp015278125	82.0287	814	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938205.1	s__Vibrio panuliri	81.5604	801	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_000222605.1	s__Vibrio ichthyoenteri	81.1431	617	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222585.1	s__Vibrio scophthalmi	81.0894	654	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_009938165.1	s__Vibrio taketomensis	81.0739	691	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_000827885.1	s__Vibrio renipiscarius	80.7085	606	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:55,774] [INFO] GTDB search result was written to GCF_014050145.1_ASM1405014v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:55,776] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:55,783] [INFO] DFAST_QC result json was written to GCF_014050145.1_ASM1405014v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:55,783] [INFO] DFAST_QC completed!
[2024-01-25 18:16:55,783] [INFO] Total running time: 0h1m5s