[2023-03-14 10:55:58,922] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b54825f-e5a9-4241-b77b-08db2536fef0/dqc_reference
[2023-03-14 10:56:00,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,680] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,680] [INFO] Running command: cat /var/lib/cwl/stgbdd4fd2d-d119-4a59-87d9-90c0756ff2fb/OceanDNA-b9655.fa | prodigal -d OceanDNA-b9655/cds.fna -a OceanDNA-b9655/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:15,123] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:15,123] [INFO] Task started: HMMsearch
[2023-03-14 10:56:15,123] [INFO] Running command: hmmsearch --tblout OceanDNA-b9655/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b54825f-e5a9-4241-b77b-08db2536fef0/dqc_reference/reference_markers.hmm OceanDNA-b9655/protein.faa > /dev/null
[2023-03-14 10:56:15,372] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:15,372] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbdd4fd2d-d119-4a59-87d9-90c0756ff2fb/OceanDNA-b9655.fa]
[2023-03-14 10:56:15,390] [INFO] Query marker FASTA was written to OceanDNA-b9655/markers.fasta
[2023-03-14 10:56:15,390] [INFO] Task started: Blastn
[2023-03-14 10:56:15,390] [INFO] Running command: blastn -query OceanDNA-b9655/markers.fasta -db /var/lib/cwl/stg6b54825f-e5a9-4241-b77b-08db2536fef0/dqc_reference/reference_markers.fasta -out OceanDNA-b9655/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:16,034] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:16,035] [INFO] Selected 20 target genomes.
[2023-03-14 10:56:16,035] [INFO] Target genome list was writen to OceanDNA-b9655/target_genomes.txt
[2023-03-14 10:56:16,045] [INFO] Task started: fastANI
[2023-03-14 10:56:16,046] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdd4fd2d-d119-4a59-87d9-90c0756ff2fb/OceanDNA-b9655.fa --refList OceanDNA-b9655/target_genomes.txt --output OceanDNA-b9655/fastani_result.tsv --threads 1
[2023-03-14 10:56:29,733] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:29,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b54825f-e5a9-4241-b77b-08db2536fef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:29,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b54825f-e5a9-4241-b77b-08db2536fef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:29,743] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:29,743] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:29,743] [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
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	78.0994	143	463	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	77.7409	125	463	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	77.6417	123	463	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	77.6394	133	463	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	77.6303	123	463	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	77.6133	120	463	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	77.5433	151	463	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	77.5232	125	463	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	77.522	127	463	95	below_threshold
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	77.4649	115	463	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	77.3922	60	463	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	77.3874	126	463	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	77.297	54	463	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	76.9699	120	463	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	76.7576	119	463	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.7439	68	463	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	76.6299	61	463	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:29,744] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9655/tc_result.tsv
[2023-03-14 10:56:29,744] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:29,744] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:29,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b54825f-e5a9-4241-b77b-08db2536fef0/dqc_reference/checkm_data
[2023-03-14 10:56:29,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:29,749] [INFO] Task started: CheckM
[2023-03-14 10:56:29,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9655/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9655/checkm_input OceanDNA-b9655/checkm_result
[2023-03-14 10:57:09,486] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:09,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.76%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:09,489] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:09,489] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:09,489] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9655/markers.fasta)
[2023-03-14 10:57:09,490] [INFO] Task started: Blastn
[2023-03-14 10:57:09,490] [INFO] Running command: blastn -query OceanDNA-b9655/markers.fasta -db /var/lib/cwl/stg6b54825f-e5a9-4241-b77b-08db2536fef0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9655/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:10,463] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:10,464] [INFO] Selected 23 target genomes.
[2023-03-14 10:57:10,464] [INFO] Target genome list was writen to OceanDNA-b9655/target_genomes_gtdb.txt
[2023-03-14 10:57:10,487] [INFO] Task started: fastANI
[2023-03-14 10:57:10,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdd4fd2d-d119-4a59-87d9-90c0756ff2fb/OceanDNA-b9655.fa --refList OceanDNA-b9655/target_genomes_gtdb.txt --output OceanDNA-b9655/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:25,849] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:25,860] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:57:25,861] [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_900167935.1	s__Maribacter arcticus	78.0994	143	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	77.7409	125	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_900155985.1	s__Maribacter ulvicola	77.6417	123	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447995.1	s__Maribacter dokdonensis	77.6394	133	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_000744105.1	s__Maribacter forsetii	77.6303	123	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	77.6133	120	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_900109345.1	s__Maribacter orientalis	77.5433	151	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	77.522	127	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003933245.1	s__Maribacter algicola	77.4649	115	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	77.4483	125	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000733925.1	s__Arenibacter algicola	77.3922	60	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_004364165.1	s__Maribacter spongiicola	77.3874	126	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259375.1	s__Arenibacter echinorum	77.297	54	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742265.1	s__Maribacter sp002742265	77.2502	108	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100785.1	s__Maribacter sp018100785	76.9763	102	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970695.1	s__Maribacter sp002742365	76.8795	99	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_900129275.1	s__Arenibacter palladensis	76.7439	68	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_009674825.1	s__Maribacter_A luteus	76.6299	61	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	76.5552	66	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927795.1	s__Saonia flava	76.5099	61	463	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:25,861] [INFO] GTDB search result was written to OceanDNA-b9655/result_gtdb.tsv
[2023-03-14 10:57:25,861] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:25,863] [INFO] DFAST_QC result json was written to OceanDNA-b9655/dqc_result.json
[2023-03-14 10:57:25,863] [INFO] DFAST_QC completed!
[2023-03-14 10:57:25,863] [INFO] Total running time: 0h1m27s