[2023-03-15 21:57:40,312] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:57:40,314] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:57:40,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ea08bc8-a84d-44a8-9460-09978c2a940e/dqc_reference
[2023-03-15 21:57:41,424] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:57:41,424] [INFO] Task started: Prodigal
[2023-03-15 21:57:41,424] [INFO] Running command: cat /var/lib/cwl/stg2c4491eb-8264-432b-853b-0b77ca936035/OceanDNA-b35294.fa | prodigal -d OceanDNA-b35294/cds.fna -a OceanDNA-b35294/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:58:09,009] [INFO] Task succeeded: Prodigal
[2023-03-15 21:58:09,009] [INFO] Task started: HMMsearch
[2023-03-15 21:58:09,009] [INFO] Running command: hmmsearch --tblout OceanDNA-b35294/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ea08bc8-a84d-44a8-9460-09978c2a940e/dqc_reference/reference_markers.hmm OceanDNA-b35294/protein.faa > /dev/null
[2023-03-15 21:58:09,280] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:58:09,281] [INFO] Found 6/6 markers.
[2023-03-15 21:58:09,325] [INFO] Query marker FASTA was written to OceanDNA-b35294/markers.fasta
[2023-03-15 21:58:09,326] [INFO] Task started: Blastn
[2023-03-15 21:58:09,326] [INFO] Running command: blastn -query OceanDNA-b35294/markers.fasta -db /var/lib/cwl/stg7ea08bc8-a84d-44a8-9460-09978c2a940e/dqc_reference/reference_markers.fasta -out OceanDNA-b35294/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:58:10,082] [INFO] Task succeeded: Blastn
[2023-03-15 21:58:10,122] [INFO] Selected 13 target genomes.
[2023-03-15 21:58:10,122] [INFO] Target genome list was writen to OceanDNA-b35294/target_genomes.txt
[2023-03-15 21:58:10,175] [INFO] Task started: fastANI
[2023-03-15 21:58:10,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c4491eb-8264-432b-853b-0b77ca936035/OceanDNA-b35294.fa --refList OceanDNA-b35294/target_genomes.txt --output OceanDNA-b35294/fastani_result.tsv --threads 1
[2023-03-15 21:58:24,017] [INFO] Task succeeded: fastANI
[2023-03-15 21:58:24,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ea08bc8-a84d-44a8-9460-09978c2a940e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:58:24,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ea08bc8-a84d-44a8-9460-09978c2a940e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:58:24,026] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2023-03-15 21:58:24,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 21:58:24,026] [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 alginolyticus	strain=NBRC 15630	GCA_000467145.1	663	663	type	True	98.561	1509	1599	95	conclusive
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	98.5566	1529	1599	95	conclusive
Vibrio alginolyticus	strain=ATCC 17749	GCA_000354175.2	663	663	type	True	98.5554	1527	1599	95	conclusive
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	98.5456	1515	1599	95	conclusive
Vibrio antiquarius	strain=EX25	GCA_000024825.1	150340	150340	suspected-type	True	92.5388	1415	1599	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000152485.1	150340	150340	suspected-type	True	92.296	1328	1599	95	below_threshold
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	84.874	1036	1599	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	83.9555	920	1599	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	82.5885	869	1599	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.1001	411	1599	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.8392	446	1599	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.772	382	1599	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.7711	379	1599	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:58:24,038] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35294/tc_result.tsv
[2023-03-15 21:58:24,056] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:58:24,056] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:58:24,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ea08bc8-a84d-44a8-9460-09978c2a940e/dqc_reference/checkm_data
[2023-03-15 21:58:24,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:58:24,149] [INFO] Task started: CheckM
[2023-03-15 21:58:24,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35294/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35294/checkm_input OceanDNA-b35294/checkm_result
[2023-03-15 21:59:33,609] [INFO] Task succeeded: CheckM
[2023-03-15 21:59:33,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:59:33,852] [INFO] ===== Completeness check finished =====
[2023-03-15 21:59:33,852] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:59:33,852] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35294/markers.fasta)
[2023-03-15 21:59:33,853] [INFO] Task started: Blastn
[2023-03-15 21:59:33,853] [INFO] Running command: blastn -query OceanDNA-b35294/markers.fasta -db /var/lib/cwl/stg7ea08bc8-a84d-44a8-9460-09978c2a940e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35294/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:59:34,983] [INFO] Task succeeded: Blastn
[2023-03-15 21:59:35,027] [INFO] Selected 13 target genomes.
[2023-03-15 21:59:35,027] [INFO] Target genome list was writen to OceanDNA-b35294/target_genomes_gtdb.txt
[2023-03-15 21:59:35,119] [INFO] Task started: fastANI
[2023-03-15 21:59:35,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c4491eb-8264-432b-853b-0b77ca936035/OceanDNA-b35294.fa --refList OceanDNA-b35294/target_genomes_gtdb.txt --output OceanDNA-b35294/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:59:48,711] [INFO] Task succeeded: fastANI
[2023-03-15 21:59:48,719] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:59:48,719] [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_000354175.2	s__Vibrio alginolyticus	98.5554	1527	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	conclusive
GCA_001048675.1	s__Vibrio diabolicus	92.5549	1409	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_900460535.1	s__Vibrio parahaemolyticus	86.0214	1189	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCF_000817815.1	s__Vibrio owensii	84.8716	1036	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_002563795.1	s__Vibrio sp002563795	84.3659	982	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163755.1	s__Vibrio campbellii	84.3016	982	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_000400365.1	s__Vibrio jasicida	84.2617	1033	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_001591145.1	s__Vibrio harveyi	84.2384	999	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_002741985.1	s__Vibrio rotiferianus	83.957	920	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000417905.1	s__Vibrio natriegens	82.6067	849	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
GCA_018222805.1	s__Vibrio sp018222805	82.4405	769	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000830505.1	s__Vibrio mytili	81.6888	707	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591105.1	s__Vibrio nereis	80.9106	432	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:59:48,736] [INFO] GTDB search result was written to OceanDNA-b35294/result_gtdb.tsv
[2023-03-15 21:59:48,761] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:59:48,779] [INFO] DFAST_QC result json was written to OceanDNA-b35294/dqc_result.json
[2023-03-15 21:59:48,779] [INFO] DFAST_QC completed!
[2023-03-15 21:59:48,779] [INFO] Total running time: 0h2m8s