[2023-03-18 07:58:06,153] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:58:06,153] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:58:06,153] [INFO] DQC Reference Directory: /var/lib/cwl/stga4b05f7c-3dd3-4c45-bca4-7ba85705e848/dqc_reference
[2023-03-18 07:58:07,248] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:58:07,248] [INFO] Task started: Prodigal
[2023-03-18 07:58:07,248] [INFO] Running command: cat /var/lib/cwl/stg037f2ab1-f502-4f82-a204-a87359343147/OceanDNA-b9656.fa | prodigal -d OceanDNA-b9656/cds.fna -a OceanDNA-b9656/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:58:26,194] [INFO] Task succeeded: Prodigal
[2023-03-18 07:58:26,194] [INFO] Task started: HMMsearch
[2023-03-18 07:58:26,194] [INFO] Running command: hmmsearch --tblout OceanDNA-b9656/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4b05f7c-3dd3-4c45-bca4-7ba85705e848/dqc_reference/reference_markers.hmm OceanDNA-b9656/protein.faa > /dev/null
[2023-03-18 07:58:26,376] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:58:26,376] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg037f2ab1-f502-4f82-a204-a87359343147/OceanDNA-b9656.fa]
[2023-03-18 07:58:26,394] [INFO] Query marker FASTA was written to OceanDNA-b9656/markers.fasta
[2023-03-18 07:58:26,394] [INFO] Task started: Blastn
[2023-03-18 07:58:26,394] [INFO] Running command: blastn -query OceanDNA-b9656/markers.fasta -db /var/lib/cwl/stga4b05f7c-3dd3-4c45-bca4-7ba85705e848/dqc_reference/reference_markers.fasta -out OceanDNA-b9656/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:58:26,971] [INFO] Task succeeded: Blastn
[2023-03-18 07:58:26,972] [INFO] Selected 21 target genomes.
[2023-03-18 07:58:26,972] [INFO] Target genome list was writen to OceanDNA-b9656/target_genomes.txt
[2023-03-18 07:58:26,982] [INFO] Task started: fastANI
[2023-03-18 07:58:26,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg037f2ab1-f502-4f82-a204-a87359343147/OceanDNA-b9656.fa --refList OceanDNA-b9656/target_genomes.txt --output OceanDNA-b9656/fastani_result.tsv --threads 1
[2023-03-18 07:58:40,304] [INFO] Task succeeded: fastANI
[2023-03-18 07:58:40,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4b05f7c-3dd3-4c45-bca4-7ba85705e848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:58:40,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4b05f7c-3dd3-4c45-bca4-7ba85705e848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:58:40,314] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:58:40,314] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:58:40,314] [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 antarcticus	strain=DSM 21422	GCA_000621125.1	505250	505250	type	True	89.2349	761	900	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	76.9969	135	900	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.9606	153	900	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	76.9389	159	900	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	76.863	179	900	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	76.7965	150	900	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.7816	148	900	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.7528	152	900	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	76.5179	160	900	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	76.5103	101	900	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	76.4782	64	900	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.475	97	900	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	76.4452	104	900	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	76.3436	109	900	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	76.3046	110	900	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.1443	103	900	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	75.95	70	900	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:58:40,315] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9656/tc_result.tsv
[2023-03-18 07:58:40,315] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:58:40,315] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:58:40,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4b05f7c-3dd3-4c45-bca4-7ba85705e848/dqc_reference/checkm_data
[2023-03-18 07:58:40,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:58:40,320] [INFO] Task started: CheckM
[2023-03-18 07:58:40,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9656/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9656/checkm_input OceanDNA-b9656/checkm_result
[2023-03-18 07:59:28,723] [INFO] Task succeeded: CheckM
[2023-03-18 07:59:28,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:59:28,725] [INFO] ===== Completeness check finished =====
[2023-03-18 07:59:28,725] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:59:28,726] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9656/markers.fasta)
[2023-03-18 07:59:28,726] [INFO] Task started: Blastn
[2023-03-18 07:59:28,726] [INFO] Running command: blastn -query OceanDNA-b9656/markers.fasta -db /var/lib/cwl/stga4b05f7c-3dd3-4c45-bca4-7ba85705e848/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9656/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:59:29,619] [INFO] Task succeeded: Blastn
[2023-03-18 07:59:29,620] [INFO] Selected 20 target genomes.
[2023-03-18 07:59:29,620] [INFO] Target genome list was writen to OceanDNA-b9656/target_genomes_gtdb.txt
[2023-03-18 07:59:29,636] [INFO] Task started: fastANI
[2023-03-18 07:59:29,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg037f2ab1-f502-4f82-a204-a87359343147/OceanDNA-b9656.fa --refList OceanDNA-b9656/target_genomes_gtdb.txt --output OceanDNA-b9656/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:59:43,288] [INFO] Task succeeded: fastANI
[2023-03-18 07:59:43,299] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:59:43,299] [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_000621125.1	s__Maribacter antarcticus	89.2184	762	900	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	77.0948	180	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_003075045.1	s__Maribacter litoralis	76.9941	136	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_001447995.1	s__Maribacter dokdonensis	76.9431	155	900	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	76.9243	160	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	76.863	179	900	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	76.8091	161	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900155985.1	s__Maribacter ulvicola	76.7809	152	900	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	76.7519	153	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004364165.1	s__Maribacter spongiicola	76.5179	160	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005943945.1	s__F202Z8 sp005943945	76.4782	64	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__F202Z8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386635.1	s__Maribacter flavus	76.4468	105	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_009649685.1	s__Aurantibacter_A sp009649685	76.3833	76	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269385.1	s__Maribacter cobaltidurans	76.3074	111	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016811105.1	s__Aurantibacter_A crassamenti	76.2388	94	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153165.2	s__Maribacter_A sp000153165	76.1806	82	900	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_900176415.1	s__Cellulophaga tyrosinoxydans	76.1443	103	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.0574	97	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581615.1	s__Muricauda lutimaris	75.95	70	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909235.1	s__Arenibacter catalasegens	75.7395	94	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:59:43,300] [INFO] GTDB search result was written to OceanDNA-b9656/result_gtdb.tsv
[2023-03-18 07:59:43,300] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:59:43,302] [INFO] DFAST_QC result json was written to OceanDNA-b9656/dqc_result.json
[2023-03-18 07:59:43,302] [INFO] DFAST_QC completed!
[2023-03-18 07:59:43,302] [INFO] Total running time: 0h1m37s