[2023-03-14 15:02:46,517] [INFO] DFAST_QC pipeline started.
[2023-03-14 15:02:46,517] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 15:02:46,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgb590f553-48c7-42f9-81b5-211f2d2b7b94/dqc_reference
[2023-03-14 15:02:47,656] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 15:02:47,657] [INFO] Task started: Prodigal
[2023-03-14 15:02:47,657] [INFO] Running command: cat /var/lib/cwl/stg8023d1fd-1ec7-445a-80b1-fb144344cc04/OceanDNA-b7449.fa | prodigal -d OceanDNA-b7449/cds.fna -a OceanDNA-b7449/protein.faa -g 11 -q > /dev/null
[2023-03-14 15:03:22,327] [INFO] Task succeeded: Prodigal
[2023-03-14 15:03:22,327] [INFO] Task started: HMMsearch
[2023-03-14 15:03:22,327] [INFO] Running command: hmmsearch --tblout OceanDNA-b7449/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb590f553-48c7-42f9-81b5-211f2d2b7b94/dqc_reference/reference_markers.hmm OceanDNA-b7449/protein.faa > /dev/null
[2023-03-14 15:03:22,546] [INFO] Task succeeded: HMMsearch
[2023-03-14 15:03:22,547] [INFO] Found 6/6 markers.
[2023-03-14 15:03:22,573] [INFO] Query marker FASTA was written to OceanDNA-b7449/markers.fasta
[2023-03-14 15:03:22,574] [INFO] Task started: Blastn
[2023-03-14 15:03:22,574] [INFO] Running command: blastn -query OceanDNA-b7449/markers.fasta -db /var/lib/cwl/stgb590f553-48c7-42f9-81b5-211f2d2b7b94/dqc_reference/reference_markers.fasta -out OceanDNA-b7449/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:03:23,118] [INFO] Task succeeded: Blastn
[2023-03-14 15:03:23,118] [INFO] Selected 22 target genomes.
[2023-03-14 15:03:23,119] [INFO] Target genome list was writen to OceanDNA-b7449/target_genomes.txt
[2023-03-14 15:03:23,128] [INFO] Task started: fastANI
[2023-03-14 15:03:23,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg8023d1fd-1ec7-445a-80b1-fb144344cc04/OceanDNA-b7449.fa --refList OceanDNA-b7449/target_genomes.txt --output OceanDNA-b7449/fastani_result.tsv --threads 1
[2023-03-14 15:03:40,896] [INFO] Task succeeded: fastANI
[2023-03-14 15:03:40,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb590f553-48c7-42f9-81b5-211f2d2b7b94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 15:03:40,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb590f553-48c7-42f9-81b5-211f2d2b7b94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 15:03:40,908] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 15:03:40,909] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 15:03:40,909] [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
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	84.0397	1157	1565	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	77.6308	182	1565	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	77.0952	175	1565	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	77.0566	140	1565	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	77.0029	139	1565	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	76.5114	137	1565	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	76.4505	144	1565	95	below_threshold
Eudoraea adriatica	strain=DSM 19308	GCA_000382125.1	446681	446681	type	True	76.3938	74	1565	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	76.3649	128	1565	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	76.3294	131	1565	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.1427	55	1565	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.1126	85	1565	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	76.0778	125	1565	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.0771	73	1565	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.0658	89	1565	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	75.991	67	1565	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	75.9462	78	1565	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	75.9245	73	1565	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 15:03:40,909] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7449/tc_result.tsv
[2023-03-14 15:03:40,909] [INFO] ===== Taxonomy check completed =====
[2023-03-14 15:03:40,909] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 15:03:40,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb590f553-48c7-42f9-81b5-211f2d2b7b94/dqc_reference/checkm_data
[2023-03-14 15:03:40,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 15:03:40,917] [INFO] Task started: CheckM
[2023-03-14 15:03:40,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7449/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7449/checkm_input OceanDNA-b7449/checkm_result
[2023-03-14 15:05:26,858] [INFO] Task succeeded: CheckM
[2023-03-14 15:05:26,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 15:05:26,862] [INFO] ===== Completeness check finished =====
[2023-03-14 15:05:26,862] [INFO] ===== Start GTDB Search =====
[2023-03-14 15:05:26,862] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7449/markers.fasta)
[2023-03-14 15:05:26,862] [INFO] Task started: Blastn
[2023-03-14 15:05:26,862] [INFO] Running command: blastn -query OceanDNA-b7449/markers.fasta -db /var/lib/cwl/stgb590f553-48c7-42f9-81b5-211f2d2b7b94/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7449/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:05:28,700] [INFO] Task succeeded: Blastn
[2023-03-14 15:05:28,700] [INFO] Selected 24 target genomes.
[2023-03-14 15:05:28,701] [INFO] Target genome list was writen to OceanDNA-b7449/target_genomes_gtdb.txt
[2023-03-14 15:05:28,821] [INFO] Task started: fastANI
[2023-03-14 15:05:28,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg8023d1fd-1ec7-445a-80b1-fb144344cc04/OceanDNA-b7449.fa --refList OceanDNA-b7449/target_genomes_gtdb.txt --output OceanDNA-b7449/fastani_result_gtdb.tsv --threads 1
[2023-03-14 15:05:49,580] [INFO] Task succeeded: fastANI
[2023-03-14 15:05:49,593] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 15:05:49,593] [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_900103215.1	s__Kriegella aquimaris	84.0397	1157	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kriegella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330165.1	s__Zobellia sp015330165	77.6305	182	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_009725985.1	s__Zobellia amurskyensis	77.0819	176	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	77.0566	140	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_014596745.1	s__Maribacter_A sp014596745	76.6837	151	1565	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_008367235.1	s__Pareuzebyella sediminis	76.583	132	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pareuzebyella	95.0	99.39	99.39	0.97	0.97	2	-
GCF_013402795.1	s__Costertonia aggregata	76.5255	134	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Costertonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	76.5114	137	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_001913155.1	s__Maribacter hydrothermalis	76.4934	127	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012272855.1	s__Arenibacter sp012272855	76.4929	99	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674825.1	s__Maribacter_A luteus	76.4751	142	1565	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_014855515.1	s__Euzebyella marina	76.4453	141	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	-
GCF_000382125.1	s__Eudoraea adriatica	76.3938	74	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	76.3833	128	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014610845.1	s__Maribacter_A arenosus	76.3294	131	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232435.1	s__Aurantibacter_A sp003232435	76.2765	87	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001935.1	s__Maribacter_A sp013001935	76.2441	69	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	96.76	96.72	0.66	0.66	3	-
GCF_004804315.1	s__Muricauda sp004804315	76.1126	85	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	76.0778	125	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009901585.1	s__R33 sp009901585	75.991	67	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861125.1	s__Cellulophaga baltica_A	75.889	108	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042315.1	s__Muriicola sp013042315	75.8281	51	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	99.31	99.31	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-14 15:05:49,593] [INFO] GTDB search result was written to OceanDNA-b7449/result_gtdb.tsv
[2023-03-14 15:05:49,594] [INFO] ===== GTDB Search completed =====
[2023-03-14 15:05:49,596] [INFO] DFAST_QC result json was written to OceanDNA-b7449/dqc_result.json
[2023-03-14 15:05:49,596] [INFO] DFAST_QC completed!
[2023-03-14 15:05:49,596] [INFO] Total running time: 0h3m3s