[2024-01-25 17:51:20,481] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:20,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:20,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3aab041-819b-4d03-8af8-b13278cb8070/dqc_reference
[2024-01-25 17:51:21,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:21,617] [INFO] Task started: Prodigal
[2024-01-25 17:51:21,617] [INFO] Running command: gunzip -c /var/lib/cwl/stgc473db23-067f-439d-9b8d-a374fea18f5e/GCF_024347675.1_ASM2434767v1_genomic.fna.gz | prodigal -d GCF_024347675.1_ASM2434767v1_genomic.fna/cds.fna -a GCF_024347675.1_ASM2434767v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:31,547] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:31,547] [INFO] Task started: HMMsearch
[2024-01-25 17:51:31,547] [INFO] Running command: hmmsearch --tblout GCF_024347675.1_ASM2434767v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3aab041-819b-4d03-8af8-b13278cb8070/dqc_reference/reference_markers.hmm GCF_024347675.1_ASM2434767v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:31,783] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:31,784] [INFO] Found 6/6 markers.
[2024-01-25 17:51:31,827] [INFO] Query marker FASTA was written to GCF_024347675.1_ASM2434767v1_genomic.fna/markers.fasta
[2024-01-25 17:51:31,827] [INFO] Task started: Blastn
[2024-01-25 17:51:31,827] [INFO] Running command: blastn -query GCF_024347675.1_ASM2434767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3aab041-819b-4d03-8af8-b13278cb8070/dqc_reference/reference_markers.fasta -out GCF_024347675.1_ASM2434767v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:32,597] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:32,600] [INFO] Selected 21 target genomes.
[2024-01-25 17:51:32,600] [INFO] Target genome list was writen to GCF_024347675.1_ASM2434767v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:32,645] [INFO] Task started: fastANI
[2024-01-25 17:51:32,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgc473db23-067f-439d-9b8d-a374fea18f5e/GCF_024347675.1_ASM2434767v1_genomic.fna.gz --refList GCF_024347675.1_ASM2434767v1_genomic.fna/target_genomes.txt --output GCF_024347675.1_ASM2434767v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:51,071] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:51,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3aab041-819b-4d03-8af8-b13278cb8070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:51,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3aab041-819b-4d03-8af8-b13278cb8070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:51,084] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:51,085] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:51,085] [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 ishigakensis	strain=JCM 19231	GCA_024347675.1	1481914	1481914	type	True	100.0	1594	1594	95	conclusive
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	80.9607	470	1594	95	below_threshold
Vibrio gallicus	strain=CIP 107863	GCA_024346875.1	190897	190897	type	True	80.568	459	1594	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.4828	300	1594	95	below_threshold
Vibrio comitans	strain=NBRC 102076	GCA_006538565.1	413401	413401	type	True	80.4377	457	1594	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	80.4213	250	1594	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	80.3848	280	1594	95	below_threshold
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	80.3487	232	1594	95	below_threshold
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	80.2856	417	1594	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	80.2821	307	1594	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.2692	291	1594	95	below_threshold
Vibrio superstes	strain=G3-29	GCA_003569005.1	198815	198815	type	True	80.2593	469	1594	95	below_threshold
Vibrio superstes	strain=NBRC 103154	GCA_007990955.1	198815	198815	type	True	80.2075	441	1594	95	below_threshold
Vibrio hangzhouensis	strain=CGMCC 1.7062	GCA_900107935.1	462991	462991	type	True	79.8627	222	1594	95	below_threshold
Vibrio inusitatus	strain=NBRC 102082	GCA_006538525.1	413402	413402	type	True	79.8384	399	1594	95	below_threshold
Vibrio nigripulchritudo	strain=ATCC 27043	GCA_000222685.2	28173	28173	type	True	79.7993	192	1594	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	79.7264	235	1594	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	79.6973	264	1594	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	79.6612	234	1594	95	below_threshold
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	79.5081	302	1594	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	79.2739	192	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:51,087] [INFO] DFAST Taxonomy check result was written to GCF_024347675.1_ASM2434767v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:51,087] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:51,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:51,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3aab041-819b-4d03-8af8-b13278cb8070/dqc_reference/checkm_data
[2024-01-25 17:51:51,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:51,136] [INFO] Task started: CheckM
[2024-01-25 17:51:51,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347675.1_ASM2434767v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347675.1_ASM2434767v1_genomic.fna/checkm_input GCF_024347675.1_ASM2434767v1_genomic.fna/checkm_result
[2024-01-25 17:52:24,204] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:24,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:24,227] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:24,227] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:24,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347675.1_ASM2434767v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:24,229] [INFO] Task started: Blastn
[2024-01-25 17:52:24,229] [INFO] Running command: blastn -query GCF_024347675.1_ASM2434767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3aab041-819b-4d03-8af8-b13278cb8070/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347675.1_ASM2434767v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:25,417] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:25,420] [INFO] Selected 18 target genomes.
[2024-01-25 17:52:25,420] [INFO] Target genome list was writen to GCF_024347675.1_ASM2434767v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:25,442] [INFO] Task started: fastANI
[2024-01-25 17:52:25,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgc473db23-067f-439d-9b8d-a374fea18f5e/GCF_024347675.1_ASM2434767v1_genomic.fna.gz --refList GCF_024347675.1_ASM2434767v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347675.1_ASM2434767v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:41,804] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:41,815] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:41,815] [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_000830415.1	s__Vibrio ishigakensis	99.8196	1427	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.42	95.17	0.89	0.89	4	conclusive
GCF_002163755.1	s__Vibrio campbellii	80.5536	286	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_001677275.1	s__Vibrio breoganii	80.4507	465	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.22	96.88	0.90	0.86	59	-
GCF_000176235.1	s__Vibrio orientalis	80.4401	250	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006538565.1	s__Vibrio comitans	80.4377	457	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001695575.1	s__Vibrio europaeus	80.3603	258	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_009938225.1	s__Vibrio ponticus	80.3308	229	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_003569005.1	s__Vibrio superstes	80.2617	469	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000695685.1	s__Vibrio fortis	79.9009	291	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_003970425.1	s__Vibrio penaeicida	79.8507	167	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.14	96.14	0.85	0.85	2	-
GCF_900107935.1	s__Vibrio hangzhouensis	79.8473	223	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538525.1	s__Vibrio inusitatus	79.8384	399	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222685.1	s__Vibrio nigripulchritudo	79.8146	191	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.90	96.77	0.92	0.87	18	-
GCF_002741985.1	s__Vibrio rotiferianus	79.7678	273	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_001274785.1	s__Vibrio hepatarius	79.7465	232	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_003350325.1	s__Vibrio rhodolitus	79.644	233	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_000817815.1	s__Vibrio owensii	79.5081	302	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_015278125.1	s__Vibrio sp015278125	79.3854	214	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:41,817] [INFO] GTDB search result was written to GCF_024347675.1_ASM2434767v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:41,817] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:41,821] [INFO] DFAST_QC result json was written to GCF_024347675.1_ASM2434767v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:41,821] [INFO] DFAST_QC completed!
[2024-01-25 17:52:41,821] [INFO] Total running time: 0h1m21s