[2023-03-17 03:50:15,874] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:15,874] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:15,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f0dea2a-58b2-4996-b182-81639be4c47b/dqc_reference
[2023-03-17 03:50:17,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:17,010] [INFO] Task started: Prodigal
[2023-03-17 03:50:17,010] [INFO] Running command: cat /var/lib/cwl/stg84df01a3-e979-47fe-a858-2f20cc39a6c4/OceanDNA-b10231.fa | prodigal -d OceanDNA-b10231/cds.fna -a OceanDNA-b10231/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:28,555] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:28,555] [INFO] Task started: HMMsearch
[2023-03-17 03:50:28,555] [INFO] Running command: hmmsearch --tblout OceanDNA-b10231/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f0dea2a-58b2-4996-b182-81639be4c47b/dqc_reference/reference_markers.hmm OceanDNA-b10231/protein.faa > /dev/null
[2023-03-17 03:50:28,753] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:28,754] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg84df01a3-e979-47fe-a858-2f20cc39a6c4/OceanDNA-b10231.fa]
[2023-03-17 03:50:28,768] [INFO] Query marker FASTA was written to OceanDNA-b10231/markers.fasta
[2023-03-17 03:50:28,769] [INFO] Task started: Blastn
[2023-03-17 03:50:28,769] [INFO] Running command: blastn -query OceanDNA-b10231/markers.fasta -db /var/lib/cwl/stg2f0dea2a-58b2-4996-b182-81639be4c47b/dqc_reference/reference_markers.fasta -out OceanDNA-b10231/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:29,406] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:29,406] [INFO] Selected 22 target genomes.
[2023-03-17 03:50:29,407] [INFO] Target genome list was writen to OceanDNA-b10231/target_genomes.txt
[2023-03-17 03:50:29,414] [INFO] Task started: fastANI
[2023-03-17 03:50:29,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg84df01a3-e979-47fe-a858-2f20cc39a6c4/OceanDNA-b10231.fa --refList OceanDNA-b10231/target_genomes.txt --output OceanDNA-b10231/fastani_result.tsv --threads 1
[2023-03-17 03:50:41,541] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:41,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f0dea2a-58b2-4996-b182-81639be4c47b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:41,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f0dea2a-58b2-4996-b182-81639be4c47b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:41,554] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:41,554] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:50:41,555] [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
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.6441	199	620	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.6354	197	620	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	77.5237	202	620	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.4836	205	620	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.4751	195	620	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	77.4477	209	620	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	77.4466	205	620	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.4238	196	620	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	77.4144	217	620	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	77.4041	215	620	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.3975	187	620	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.3762	228	620	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.3591	182	620	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.3424	207	620	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.3269	217	620	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	77.3145	206	620	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.2607	184	620	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.2527	199	620	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.0735	168	620	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.0367	200	620	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	77.0276	177	620	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	76.7862	150	620	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:50:41,555] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10231/tc_result.tsv
[2023-03-17 03:50:41,555] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:41,555] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:41,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f0dea2a-58b2-4996-b182-81639be4c47b/dqc_reference/checkm_data
[2023-03-17 03:50:41,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:41,559] [INFO] Task started: CheckM
[2023-03-17 03:50:41,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10231/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10231/checkm_input OceanDNA-b10231/checkm_result
[2023-03-17 03:51:14,012] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:14,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:14,015] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:14,015] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:14,015] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10231/markers.fasta)
[2023-03-17 03:51:14,015] [INFO] Task started: Blastn
[2023-03-17 03:51:14,015] [INFO] Running command: blastn -query OceanDNA-b10231/markers.fasta -db /var/lib/cwl/stg2f0dea2a-58b2-4996-b182-81639be4c47b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10231/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:14,939] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:14,940] [INFO] Selected 12 target genomes.
[2023-03-17 03:51:14,940] [INFO] Target genome list was writen to OceanDNA-b10231/target_genomes_gtdb.txt
[2023-03-17 03:51:14,987] [INFO] Task started: fastANI
[2023-03-17 03:51:14,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg84df01a3-e979-47fe-a858-2f20cc39a6c4/OceanDNA-b10231.fa --refList OceanDNA-b10231/target_genomes_gtdb.txt --output OceanDNA-b10231/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:21,348] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:21,355] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:51:21,356] [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_018608485.1	s__SCGC-AAA160-P02 sp018608485	96.3742	452	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	99.40	99.40	0.78	0.78	2	conclusive
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	93.3898	533	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCA_905479435.1	s__SCGC-AAA160-P02 sp905479435	82.8656	332	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	81.5664	445	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.64	95.28	0.86	0.84	6	-
GCF_018861005.1	s__Polaribacter vadi_A	77.5209	228	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	77.5114	232	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	77.4349	210	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_001640115.1	s__Polaribacter atrinae	77.3975	187	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763215.1	s__SCGC-AAA160-P02 sp016763215	77.2426	119	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	77.1227	171	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	76.958	151	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_008124875.1	s__Tenacibaculum adriaticum	76.7862	150	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:21,356] [INFO] GTDB search result was written to OceanDNA-b10231/result_gtdb.tsv
[2023-03-17 03:51:21,356] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:21,358] [INFO] DFAST_QC result json was written to OceanDNA-b10231/dqc_result.json
[2023-03-17 03:51:21,358] [INFO] DFAST_QC completed!
[2023-03-17 03:51:21,358] [INFO] Total running time: 0h1m5s