[2023-03-16 06:54:58,968] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:54:58,971] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:54:58,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcd0a28c-b30d-489b-a527-003285966f40/dqc_reference
[2023-03-16 06:55:00,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:55:00,137] [INFO] Task started: Prodigal
[2023-03-16 06:55:00,137] [INFO] Running command: cat /var/lib/cwl/stg34f9b1f2-0379-4127-965b-1d485723ea67/OceanDNA-b9705.fa | prodigal -d OceanDNA-b9705/cds.fna -a OceanDNA-b9705/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:55:24,378] [INFO] Task succeeded: Prodigal
[2023-03-16 06:55:24,378] [INFO] Task started: HMMsearch
[2023-03-16 06:55:24,378] [INFO] Running command: hmmsearch --tblout OceanDNA-b9705/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcd0a28c-b30d-489b-a527-003285966f40/dqc_reference/reference_markers.hmm OceanDNA-b9705/protein.faa > /dev/null
[2023-03-16 06:55:24,591] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:55:24,591] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg34f9b1f2-0379-4127-965b-1d485723ea67/OceanDNA-b9705.fa]
[2023-03-16 06:55:24,654] [INFO] Query marker FASTA was written to OceanDNA-b9705/markers.fasta
[2023-03-16 06:55:24,655] [INFO] Task started: Blastn
[2023-03-16 06:55:24,656] [INFO] Running command: blastn -query OceanDNA-b9705/markers.fasta -db /var/lib/cwl/stgbcd0a28c-b30d-489b-a527-003285966f40/dqc_reference/reference_markers.fasta -out OceanDNA-b9705/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:55:25,245] [INFO] Task succeeded: Blastn
[2023-03-16 06:55:25,257] [INFO] Selected 17 target genomes.
[2023-03-16 06:55:25,258] [INFO] Target genome list was writen to OceanDNA-b9705/target_genomes.txt
[2023-03-16 06:55:25,267] [INFO] Task started: fastANI
[2023-03-16 06:55:25,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg34f9b1f2-0379-4127-965b-1d485723ea67/OceanDNA-b9705.fa --refList OceanDNA-b9705/target_genomes.txt --output OceanDNA-b9705/fastani_result.tsv --threads 1
[2023-03-16 06:55:37,981] [INFO] Task succeeded: fastANI
[2023-03-16 06:55:37,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcd0a28c-b30d-489b-a527-003285966f40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:55:37,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcd0a28c-b30d-489b-a527-003285966f40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:55:37,991] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 06:55:37,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 06:55:37,991] [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 luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	98.1626	1020	1070	95	conclusive
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	81.6747	724	1070	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	81.647	736	1070	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	78.7081	418	1070	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	76.8711	144	1070	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.5486	134	1070	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.4671	114	1070	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.4108	116	1070	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	76.2942	135	1070	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	76.2632	95	1070	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	76.1187	124	1070	95	below_threshold
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	76.0675	111	1070	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.0672	58	1070	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	75.8307	56	1070	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	75.7368	62	1070	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:55:37,996] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9705/tc_result.tsv
[2023-03-16 06:55:38,002] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:55:38,002] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:55:38,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcd0a28c-b30d-489b-a527-003285966f40/dqc_reference/checkm_data
[2023-03-16 06:55:38,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:55:38,010] [INFO] Task started: CheckM
[2023-03-16 06:55:38,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9705/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9705/checkm_input OceanDNA-b9705/checkm_result
[2023-03-16 06:56:39,364] [INFO] Task succeeded: CheckM
[2023-03-16 06:56:39,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:56:39,474] [INFO] ===== Completeness check finished =====
[2023-03-16 06:56:39,474] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:56:39,474] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9705/markers.fasta)
[2023-03-16 06:56:39,475] [INFO] Task started: Blastn
[2023-03-16 06:56:39,475] [INFO] Running command: blastn -query OceanDNA-b9705/markers.fasta -db /var/lib/cwl/stgbcd0a28c-b30d-489b-a527-003285966f40/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9705/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:56:40,237] [INFO] Task succeeded: Blastn
[2023-03-16 06:56:40,242] [INFO] Selected 12 target genomes.
[2023-03-16 06:56:40,242] [INFO] Target genome list was writen to OceanDNA-b9705/target_genomes_gtdb.txt
[2023-03-16 06:56:40,255] [INFO] Task started: fastANI
[2023-03-16 06:56:40,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg34f9b1f2-0379-4127-965b-1d485723ea67/OceanDNA-b9705.fa --refList OceanDNA-b9705/target_genomes_gtdb.txt --output OceanDNA-b9705/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:56:48,512] [INFO] Task succeeded: fastANI
[2023-03-16 06:56:48,520] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:56:48,520] [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_009674825.1	s__Maribacter_A luteus	98.1626	1020	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148665.1	s__Maribacter_A polysiphoniae	81.6747	724	1070	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	80.6638	704	1070	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_002749285.1	s__Maribacter_A sp002749285	78.8064	308	1070	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_014610845.1	s__Maribacter_A arenosus	78.7186	417	1070	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_000153165.2	s__Maribacter_A sp000153165	77.7769	275	1070	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_018679695.1	s__Maribacter_A sp018679695	77.721	231	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.00	99.00	0.82	0.82	2	-
GCA_013001935.1	s__Maribacter_A sp013001935	77.7032	132	1070	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_001913155.1	s__Maribacter hydrothermalis	76.4108	116	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009725995.1	s__Zobellia laminariae	76.2942	135	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	76.0967	78	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	76.0912	126	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:56:48,522] [INFO] GTDB search result was written to OceanDNA-b9705/result_gtdb.tsv
[2023-03-16 06:56:48,524] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:56:48,526] [INFO] DFAST_QC result json was written to OceanDNA-b9705/dqc_result.json
[2023-03-16 06:56:48,526] [INFO] DFAST_QC completed!
[2023-03-16 06:56:48,526] [INFO] Total running time: 0h1m50s