[2024-01-24 14:05:36,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ca98c44-5bf0-4af9-89c0-b6c2e5fd1d12/dqc_reference
[2024-01-24 14:05:38,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:38,005] [INFO] Task started: Prodigal
[2024-01-24 14:05:38,006] [INFO] Running command: gunzip -c /var/lib/cwl/stgb934654e-4c82-4abd-a083-2a05f19bae98/GCF_003970385.1_ASM397038v1_genomic.fna.gz | prodigal -d GCF_003970385.1_ASM397038v1_genomic.fna/cds.fna -a GCF_003970385.1_ASM397038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:48,731] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:48,731] [INFO] Task started: HMMsearch
[2024-01-24 14:05:48,731] [INFO] Running command: hmmsearch --tblout GCF_003970385.1_ASM397038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ca98c44-5bf0-4af9-89c0-b6c2e5fd1d12/dqc_reference/reference_markers.hmm GCF_003970385.1_ASM397038v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:49,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:49,102] [INFO] Found 6/6 markers.
[2024-01-24 14:05:49,141] [INFO] Query marker FASTA was written to GCF_003970385.1_ASM397038v1_genomic.fna/markers.fasta
[2024-01-24 14:05:49,141] [INFO] Task started: Blastn
[2024-01-24 14:05:49,141] [INFO] Running command: blastn -query GCF_003970385.1_ASM397038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ca98c44-5bf0-4af9-89c0-b6c2e5fd1d12/dqc_reference/reference_markers.fasta -out GCF_003970385.1_ASM397038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:50,037] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:50,040] [INFO] Selected 14 target genomes.
[2024-01-24 14:05:50,041] [INFO] Target genome list was writen to GCF_003970385.1_ASM397038v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:50,044] [INFO] Task started: fastANI
[2024-01-24 14:05:50,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgb934654e-4c82-4abd-a083-2a05f19bae98/GCF_003970385.1_ASM397038v1_genomic.fna.gz --refList GCF_003970385.1_ASM397038v1_genomic.fna/target_genomes.txt --output GCF_003970385.1_ASM397038v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:03,861] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:03,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ca98c44-5bf0-4af9-89c0-b6c2e5fd1d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:03,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ca98c44-5bf0-4af9-89c0-b6c2e5fd1d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:03,881] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:03,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:03,882] [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 aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	100.0	1431	1433	95	conclusive
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	83.7179	944	1433	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	83.6346	929	1433	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	82.2481	748	1433	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	82.1915	731	1433	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	82.1102	780	1433	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	81.8705	728	1433	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.7777	474	1433	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	80.7111	494	1433	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	80.4286	496	1433	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	80.3229	500	1433	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.3183	438	1433	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.3123	438	1433	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.2222	427	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:03,883] [INFO] DFAST Taxonomy check result was written to GCF_003970385.1_ASM397038v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:03,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:03,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:03,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ca98c44-5bf0-4af9-89c0-b6c2e5fd1d12/dqc_reference/checkm_data
[2024-01-24 14:06:03,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:03,932] [INFO] Task started: CheckM
[2024-01-24 14:06:03,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970385.1_ASM397038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970385.1_ASM397038v1_genomic.fna/checkm_input GCF_003970385.1_ASM397038v1_genomic.fna/checkm_result
[2024-01-24 14:06:42,722] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:42,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:42,753] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:42,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:42,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970385.1_ASM397038v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:42,755] [INFO] Task started: Blastn
[2024-01-24 14:06:42,755] [INFO] Running command: blastn -query GCF_003970385.1_ASM397038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ca98c44-5bf0-4af9-89c0-b6c2e5fd1d12/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970385.1_ASM397038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:44,072] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:44,076] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:44,077] [INFO] Target genome list was writen to GCF_003970385.1_ASM397038v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:44,090] [INFO] Task started: fastANI
[2024-01-24 14:06:44,090] [INFO] Running command: fastANI --query /var/lib/cwl/stgb934654e-4c82-4abd-a083-2a05f19bae98/GCF_003970385.1_ASM397038v1_genomic.fna.gz --refList GCF_003970385.1_ASM397038v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970385.1_ASM397038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:56,855] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:56,871] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:56,872] [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_003970385.1	s__Vibrio aquaticus	100.0	1431	1433	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_004551525.1	s__Vibrio ouci	84.4655	956	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176235.1	s__Vibrio orientalis	83.6993	946	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013114545.1	s__Vibrio sp013114545	83.0924	825	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772105.1	s__Vibrio tubiashii	82.2637	746	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_001695575.1	s__Vibrio europaeus	82.1027	781	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000808535.1	s__Vibrio sinaloensis	82.1009	652	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_009811315.1	s__Vibrio atypicus	81.9328	697	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_001399455.2	s__Vibrio bivalvicida	81.8579	727	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_000189275.1	s__Vibrio sinaloensis_B	81.795	648	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006124995.1	s__Vibrio sp006124995	81.6615	669	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967495.1	s__Vibrio neptunius	80.7965	527	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:56,873] [INFO] GTDB search result was written to GCF_003970385.1_ASM397038v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:56,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:56,878] [INFO] DFAST_QC result json was written to GCF_003970385.1_ASM397038v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:56,878] [INFO] DFAST_QC completed!
[2024-01-24 14:06:56,878] [INFO] Total running time: 0h1m20s