[2023-03-16 07:11:53,903] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:11:53,903] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:11:53,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg50f9f494-6af4-4340-9769-9509b44f8aa0/dqc_reference
[2023-03-16 07:11:54,985] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:11:54,986] [INFO] Task started: Prodigal
[2023-03-16 07:11:54,987] [INFO] Running command: cat /var/lib/cwl/stg7a1b3203-b298-4c43-ac45-0da32e36f6e3/OceanDNA-b10114.fa | prodigal -d OceanDNA-b10114/cds.fna -a OceanDNA-b10114/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:12:07,646] [INFO] Task succeeded: Prodigal
[2023-03-16 07:12:07,646] [INFO] Task started: HMMsearch
[2023-03-16 07:12:07,646] [INFO] Running command: hmmsearch --tblout OceanDNA-b10114/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50f9f494-6af4-4340-9769-9509b44f8aa0/dqc_reference/reference_markers.hmm OceanDNA-b10114/protein.faa > /dev/null
[2023-03-16 07:12:07,844] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:12:07,844] [INFO] Found 6/6 markers.
[2023-03-16 07:12:07,861] [INFO] Query marker FASTA was written to OceanDNA-b10114/markers.fasta
[2023-03-16 07:12:07,862] [INFO] Task started: Blastn
[2023-03-16 07:12:07,862] [INFO] Running command: blastn -query OceanDNA-b10114/markers.fasta -db /var/lib/cwl/stg50f9f494-6af4-4340-9769-9509b44f8aa0/dqc_reference/reference_markers.fasta -out OceanDNA-b10114/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:12:08,441] [INFO] Task succeeded: Blastn
[2023-03-16 07:12:08,442] [INFO] Selected 23 target genomes.
[2023-03-16 07:12:08,443] [INFO] Target genome list was writen to OceanDNA-b10114/target_genomes.txt
[2023-03-16 07:12:08,484] [INFO] Task started: fastANI
[2023-03-16 07:12:08,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a1b3203-b298-4c43-ac45-0da32e36f6e3/OceanDNA-b10114.fa --refList OceanDNA-b10114/target_genomes.txt --output OceanDNA-b10114/fastani_result.tsv --threads 1
[2023-03-16 07:12:20,880] [INFO] Task succeeded: fastANI
[2023-03-16 07:12:20,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50f9f494-6af4-4340-9769-9509b44f8aa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:12:20,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50f9f494-6af4-4340-9769-9509b44f8aa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:12:20,894] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:12:20,894] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:12:20,894] [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 pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.6597	240	675	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.5999	200	675	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.4898	216	675	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.3222	220	675	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	77.316	243	675	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	77.3137	242	675	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	77.2812	248	675	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	77.2724	248	675	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.2362	216	675	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.2138	232	675	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.2005	216	675	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.2005	221	675	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.1983	229	675	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.1945	212	675	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.1655	217	675	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	77.1611	178	675	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.1548	226	675	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	77.1545	233	675	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.1067	212	675	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.9844	173	675	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.9654	171	675	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.9123	219	675	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	76.7435	144	675	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:12:20,894] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10114/tc_result.tsv
[2023-03-16 07:12:20,894] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:12:20,894] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:12:20,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50f9f494-6af4-4340-9769-9509b44f8aa0/dqc_reference/checkm_data
[2023-03-16 07:12:20,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:12:20,899] [INFO] Task started: CheckM
[2023-03-16 07:12:20,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10114/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10114/checkm_input OceanDNA-b10114/checkm_result
[2023-03-16 07:12:56,115] [INFO] Task succeeded: CheckM
[2023-03-16 07:12:56,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.24%
Contamintation: 6.25%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 07:12:56,131] [INFO] ===== Completeness check finished =====
[2023-03-16 07:12:56,131] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:12:56,131] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10114/markers.fasta)
[2023-03-16 07:12:56,132] [INFO] Task started: Blastn
[2023-03-16 07:12:56,133] [INFO] Running command: blastn -query OceanDNA-b10114/markers.fasta -db /var/lib/cwl/stg50f9f494-6af4-4340-9769-9509b44f8aa0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10114/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:12:57,121] [INFO] Task succeeded: Blastn
[2023-03-16 07:12:57,124] [INFO] Selected 16 target genomes.
[2023-03-16 07:12:57,124] [INFO] Target genome list was writen to OceanDNA-b10114/target_genomes_gtdb.txt
[2023-03-16 07:12:57,135] [INFO] Task started: fastANI
[2023-03-16 07:12:57,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a1b3203-b298-4c43-ac45-0da32e36f6e3/OceanDNA-b10114.fa --refList OceanDNA-b10114/target_genomes_gtdb.txt --output OceanDNA-b10114/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:13:06,164] [INFO] Task succeeded: fastANI
[2023-03-16 07:13:06,174] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:13:06,174] [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_000383355.1	s__SCGC-AAA160-P02 sp000383355	89.5245	509	675	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	-
GCA_905479435.1	s__SCGC-AAA160-P02 sp905479435	80.7188	321	675	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_015665265.1	s__SCGC-AAA160-P02 sp015665265	80.4985	420	675	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_018608485.1	s__SCGC-AAA160-P02 sp018608485	80.0558	337	675	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	-
GCF_002163835.1	s__Polaribacter sp002163835	77.8659	236	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	77.7191	232	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	77.6735	264	675	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	77.5647	157	675	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	-
GCF_007827455.1	s__VISM01 sp007827455	77.5508	233	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373105.1	s__Polaribacter sp013373105	77.4837	171	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861005.1	s__Polaribacter vadi_A	77.3975	246	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106075.1	s__Polaribacter sp900106075	77.2864	236	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_002005425.1	s__Polaribacter sp002005425	77.2752	230	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_009796785.1	s__Polaribacter sp009796785	77.141	232	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836595.1	s__Tenacibaculum sp002836595	77.1216	176	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	76.9793	171	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:13:06,176] [INFO] GTDB search result was written to OceanDNA-b10114/result_gtdb.tsv
[2023-03-16 07:13:06,176] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:13:06,180] [INFO] DFAST_QC result json was written to OceanDNA-b10114/dqc_result.json
[2023-03-16 07:13:06,180] [INFO] DFAST_QC completed!
[2023-03-16 07:13:06,181] [INFO] Total running time: 0h1m12s