[2023-03-17 10:16:56,379] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:16:56,379] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:16:56,379] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe73dcf8-5009-46d1-b048-1a1d95fa0e50/dqc_reference
[2023-03-17 10:16:57,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:16:57,517] [INFO] Task started: Prodigal
[2023-03-17 10:16:57,518] [INFO] Running command: cat /var/lib/cwl/stgc2ee30e6-322a-4f12-9d34-d5ed63eca79f/OceanDNA-b6704.fa | prodigal -d OceanDNA-b6704/cds.fna -a OceanDNA-b6704/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:17:17,994] [INFO] Task succeeded: Prodigal
[2023-03-17 10:17:17,994] [INFO] Task started: HMMsearch
[2023-03-17 10:17:17,994] [INFO] Running command: hmmsearch --tblout OceanDNA-b6704/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe73dcf8-5009-46d1-b048-1a1d95fa0e50/dqc_reference/reference_markers.hmm OceanDNA-b6704/protein.faa > /dev/null
[2023-03-17 10:17:18,172] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:17:18,173] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc2ee30e6-322a-4f12-9d34-d5ed63eca79f/OceanDNA-b6704.fa]
[2023-03-17 10:17:18,193] [INFO] Query marker FASTA was written to OceanDNA-b6704/markers.fasta
[2023-03-17 10:17:18,193] [INFO] Task started: Blastn
[2023-03-17 10:17:18,194] [INFO] Running command: blastn -query OceanDNA-b6704/markers.fasta -db /var/lib/cwl/stgbe73dcf8-5009-46d1-b048-1a1d95fa0e50/dqc_reference/reference_markers.fasta -out OceanDNA-b6704/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:17:18,721] [INFO] Task succeeded: Blastn
[2023-03-17 10:17:18,722] [INFO] Selected 31 target genomes.
[2023-03-17 10:17:18,723] [INFO] Target genome list was writen to OceanDNA-b6704/target_genomes.txt
[2023-03-17 10:17:18,760] [INFO] Task started: fastANI
[2023-03-17 10:17:18,760] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2ee30e6-322a-4f12-9d34-d5ed63eca79f/OceanDNA-b6704.fa --refList OceanDNA-b6704/target_genomes.txt --output OceanDNA-b6704/fastani_result.tsv --threads 1
[2023-03-17 10:17:37,480] [INFO] Task succeeded: fastANI
[2023-03-17 10:17:37,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe73dcf8-5009-46d1-b048-1a1d95fa0e50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:17:37,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe73dcf8-5009-46d1-b048-1a1d95fa0e50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:17:37,489] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:17:37,489] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:17:37,489] [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
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.5158	70	749	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	76.0368	62	749	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	76.0236	69	749	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	75.9919	71	749	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	75.9786	69	749	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	75.9785	69	749	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	75.9618	77	749	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	75.9141	68	749	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	75.9096	62	749	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	75.9096	62	749	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	75.8828	61	749	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	75.7899	69	749	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	75.7858	61	749	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	75.678	61	749	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	75.6333	50	749	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:17:37,492] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6704/tc_result.tsv
[2023-03-17 10:17:37,497] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:17:37,497] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:17:37,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe73dcf8-5009-46d1-b048-1a1d95fa0e50/dqc_reference/checkm_data
[2023-03-17 10:17:37,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:17:37,508] [INFO] Task started: CheckM
[2023-03-17 10:17:37,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6704/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6704/checkm_input OceanDNA-b6704/checkm_result
[2023-03-17 10:18:32,095] [INFO] Task succeeded: CheckM
[2023-03-17 10:18:32,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:18:32,116] [INFO] ===== Completeness check finished =====
[2023-03-17 10:18:32,117] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:18:32,117] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6704/markers.fasta)
[2023-03-17 10:18:32,118] [INFO] Task started: Blastn
[2023-03-17 10:18:32,118] [INFO] Running command: blastn -query OceanDNA-b6704/markers.fasta -db /var/lib/cwl/stgbe73dcf8-5009-46d1-b048-1a1d95fa0e50/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6704/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:18:32,843] [INFO] Task succeeded: Blastn
[2023-03-17 10:18:32,846] [INFO] Selected 30 target genomes.
[2023-03-17 10:18:32,846] [INFO] Target genome list was writen to OceanDNA-b6704/target_genomes_gtdb.txt
[2023-03-17 10:18:32,962] [INFO] Task started: fastANI
[2023-03-17 10:18:32,963] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2ee30e6-322a-4f12-9d34-d5ed63eca79f/OceanDNA-b6704.fa --refList OceanDNA-b6704/target_genomes_gtdb.txt --output OceanDNA-b6704/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:18:49,885] [INFO] Task succeeded: fastANI
[2023-03-17 10:18:49,896] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:18:49,897] [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_009797885.1	s__Croceivirga sp009797885	76.969	136	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	76.5158	70	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_003385855.1	s__Muricauda sp003385855	76.366	76	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCA_017795065.1	s__Muricauda sp017795065	76.2435	68	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001145.1	s__Croceitalea sp013001145	76.1882	69	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	99.20	99.17	0.87	0.85	5	-
GCF_017313105.1	s__Muricauda sp017313105	76.1848	59	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	76.1362	58	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.1126	60	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	76.0873	54	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214065.1	s__DT-32 sp013214065	76.0845	82	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	76.0368	55	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407935.1	s__Muricauda sp013407935	76.0329	66	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.58	96.50	0.87	0.86	8	-
GCF_003581615.1	s__Muricauda lutimaris	76.0236	69	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	75.9919	71	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003584135.1	s__Muricauda sp003584135	75.9786	69	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004916895.1	s__Muricauda alvinocaridis	75.9618	77	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	75.9587	61	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584165.1	s__Muricauda sp003584165	75.9096	62	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014698935.1	s__Muricauda sp014698935	75.8951	65	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500845.1	s__Muricauda sediminis	75.7858	61	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129665.1	s__Muricauda flava	75.678	61	749	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:18:49,898] [INFO] GTDB search result was written to OceanDNA-b6704/result_gtdb.tsv
[2023-03-17 10:18:49,899] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:18:49,902] [INFO] DFAST_QC result json was written to OceanDNA-b6704/dqc_result.json
[2023-03-17 10:18:49,902] [INFO] DFAST_QC completed!
[2023-03-17 10:18:49,902] [INFO] Total running time: 0h1m54s