[2023-03-16 18:18:12,624] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:18:12,624] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:18:12,624] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfc1b3f7-af06-491e-86a1-a1735b837e7c/dqc_reference
[2023-03-16 18:18:13,738] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:18:13,739] [INFO] Task started: Prodigal
[2023-03-16 18:18:13,739] [INFO] Running command: cat /var/lib/cwl/stg53265f7d-3431-4e34-9662-2746b6ad5aea/OceanDNA-b36635.fa | prodigal -d OceanDNA-b36635/cds.fna -a OceanDNA-b36635/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:18:44,645] [INFO] Task succeeded: Prodigal
[2023-03-16 18:18:44,645] [INFO] Task started: HMMsearch
[2023-03-16 18:18:44,645] [INFO] Running command: hmmsearch --tblout OceanDNA-b36635/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfc1b3f7-af06-491e-86a1-a1735b837e7c/dqc_reference/reference_markers.hmm OceanDNA-b36635/protein.faa > /dev/null
[2023-03-16 18:18:44,838] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:18:44,839] [INFO] Found 6/6 markers.
[2023-03-16 18:18:44,858] [INFO] Query marker FASTA was written to OceanDNA-b36635/markers.fasta
[2023-03-16 18:18:44,859] [INFO] Task started: Blastn
[2023-03-16 18:18:44,859] [INFO] Running command: blastn -query OceanDNA-b36635/markers.fasta -db /var/lib/cwl/stgbfc1b3f7-af06-491e-86a1-a1735b837e7c/dqc_reference/reference_markers.fasta -out OceanDNA-b36635/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:18:45,607] [INFO] Task succeeded: Blastn
[2023-03-16 18:18:45,608] [INFO] Selected 23 target genomes.
[2023-03-16 18:18:45,608] [INFO] Target genome list was writen to OceanDNA-b36635/target_genomes.txt
[2023-03-16 18:18:45,664] [INFO] Task started: fastANI
[2023-03-16 18:18:45,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg53265f7d-3431-4e34-9662-2746b6ad5aea/OceanDNA-b36635.fa --refList OceanDNA-b36635/target_genomes.txt --output OceanDNA-b36635/fastani_result.tsv --threads 1
[2023-03-16 18:19:00,759] [INFO] Task succeeded: fastANI
[2023-03-16 18:19:00,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfc1b3f7-af06-491e-86a1-a1735b837e7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:19:00,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfc1b3f7-af06-491e-86a1-a1735b837e7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:19:00,770] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:19:00,770] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:19:00,771] [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
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	77.9868	210	1026	95	below_threshold
Alcanivorax indicus	strain=SW127	GCA_003259185.1	2202653	2202653	type	True	77.386	202	1026	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	77.3064	146	1026	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	77.205	155	1026	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	77.1506	166	1026	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	77.1412	140	1026	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	77.1338	141	1026	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	77.0903	142	1026	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	77.016	152	1026	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	76.9996	166	1026	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	76.9025	167	1026	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	76.7078	69	1026	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.6593	69	1026	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.5673	68	1026	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.4421	84	1026	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	76.1328	57	1026	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	76.0632	69	1026	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:19:00,771] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36635/tc_result.tsv
[2023-03-16 18:19:00,771] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:19:00,771] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:19:00,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfc1b3f7-af06-491e-86a1-a1735b837e7c/dqc_reference/checkm_data
[2023-03-16 18:19:00,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:19:00,779] [INFO] Task started: CheckM
[2023-03-16 18:19:00,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36635/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36635/checkm_input OceanDNA-b36635/checkm_result
[2023-03-16 18:19:50,686] [INFO] Task succeeded: CheckM
[2023-03-16 18:19:50,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:19:50,689] [INFO] ===== Completeness check finished =====
[2023-03-16 18:19:50,689] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:19:50,690] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36635/markers.fasta)
[2023-03-16 18:19:50,691] [INFO] Task started: Blastn
[2023-03-16 18:19:50,691] [INFO] Running command: blastn -query OceanDNA-b36635/markers.fasta -db /var/lib/cwl/stgbfc1b3f7-af06-491e-86a1-a1735b837e7c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36635/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:19:51,983] [INFO] Task succeeded: Blastn
[2023-03-16 18:19:51,984] [INFO] Selected 21 target genomes.
[2023-03-16 18:19:51,984] [INFO] Target genome list was writen to OceanDNA-b36635/target_genomes_gtdb.txt
[2023-03-16 18:19:52,123] [INFO] Task started: fastANI
[2023-03-16 18:19:52,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg53265f7d-3431-4e34-9662-2746b6ad5aea/OceanDNA-b36635.fa --refList OceanDNA-b36635/target_genomes_gtdb.txt --output OceanDNA-b36635/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:20:05,998] [INFO] Task succeeded: fastANI
[2023-03-16 18:20:06,011] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:20:06,011] [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_002840115.1	s__PGZG01 sp002840115	79.8517	211	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__PGZG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299335.2	s__Alcanivorax_A pacificus	77.9868	210	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846755.1	s__Alcanivorax_A sp009846755	77.4704	209	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259185.1	s__Alcanivorax_A indicus	77.386	202	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	77.3064	146	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCA_014762765.1	s__Alcanivorax sp014762765	77.2479	150	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823245.1	s__Alcanivorax_A sp013823245	77.2439	188	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706085.1	s__Alcanivorax sp002706085	77.2237	147	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.88	0.86	0.86	2	-
GCF_900107995.1	s__Alcanivorax sp900107995	77.1651	169	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000756655.1	s__Alcanivorax jadensis	77.1506	166	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_002864685.1	s__Alcanivorax mobilis	77.1338	141	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.57	98.57	0.96	0.96	2	-
GCA_017794965.1	s__Alcanivorax sp017794965	77.1245	156	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794945.1	s__Alcanivorax sp009711585	77.0821	141	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCF_016906305.1	s__Alcanivorax marinus_B	77.0232	160	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003597125.1	s__Alcanivorax profundi	77.0142	165	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.31	99.31	0.96	0.96	2	-
GCF_000155615.1	s__Alcanivorax sp000155615	76.8543	180	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.69	0.92	0.89	4	-
GCF_016651305.1	s__Pseudomonas_E sp016651305	76.1758	58	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011755.1	s__Pseudomonas_E sp004011755	75.8992	68	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.20	98.13	0.94	0.93	4	-
GCF_016650635.1	s__Pseudomonas_E sp016650635	75.474	57	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	97.85	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-16 18:20:06,011] [INFO] GTDB search result was written to OceanDNA-b36635/result_gtdb.tsv
[2023-03-16 18:20:06,012] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:20:06,014] [INFO] DFAST_QC result json was written to OceanDNA-b36635/dqc_result.json
[2023-03-16 18:20:06,015] [INFO] DFAST_QC completed!
[2023-03-16 18:20:06,015] [INFO] Total running time: 0h1m53s