[2023-03-17 05:16:57,860] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:57,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:57,861] [INFO] DQC Reference Directory: /var/lib/cwl/stg1aa8f70f-3161-4834-b019-55edb38b5ae4/dqc_reference
[2023-03-17 05:16:59,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,367] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,367] [INFO] Running command: cat /var/lib/cwl/stgac682835-b987-4fc6-97a2-0670f20e09b0/OceanDNA-b7547.fa | prodigal -d OceanDNA-b7547/cds.fna -a OceanDNA-b7547/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:13,529] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:13,529] [INFO] Task started: HMMsearch
[2023-03-17 05:17:13,529] [INFO] Running command: hmmsearch --tblout OceanDNA-b7547/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1aa8f70f-3161-4834-b019-55edb38b5ae4/dqc_reference/reference_markers.hmm OceanDNA-b7547/protein.faa > /dev/null
[2023-03-17 05:17:13,717] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:13,717] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgac682835-b987-4fc6-97a2-0670f20e09b0/OceanDNA-b7547.fa]
[2023-03-17 05:17:13,732] [INFO] Query marker FASTA was written to OceanDNA-b7547/markers.fasta
[2023-03-17 05:17:13,733] [INFO] Task started: Blastn
[2023-03-17 05:17:13,733] [INFO] Running command: blastn -query OceanDNA-b7547/markers.fasta -db /var/lib/cwl/stg1aa8f70f-3161-4834-b019-55edb38b5ae4/dqc_reference/reference_markers.fasta -out OceanDNA-b7547/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:14,284] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:14,285] [INFO] Selected 11 target genomes.
[2023-03-17 05:17:14,285] [INFO] Target genome list was writen to OceanDNA-b7547/target_genomes.txt
[2023-03-17 05:17:14,323] [INFO] Task started: fastANI
[2023-03-17 05:17:14,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgac682835-b987-4fc6-97a2-0670f20e09b0/OceanDNA-b7547.fa --refList OceanDNA-b7547/target_genomes.txt --output OceanDNA-b7547/fastani_result.tsv --threads 1
[2023-03-17 05:17:20,998] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:20,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1aa8f70f-3161-4834-b019-55edb38b5ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:20,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1aa8f70f-3161-4834-b019-55edb38b5ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:21,007] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:21,007] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:17:21,007] [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
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	79.8629	476	763	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	79.8392	464	763	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	79.8065	473	763	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	79.7596	452	763	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	79.6914	505	763	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	79.4817	425	763	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.0834	202	763	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.9601	156	763	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.7775	171	763	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.4983	153	763	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.4157	164	763	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:17:21,007] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7547/tc_result.tsv
[2023-03-17 05:17:21,007] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:21,007] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:21,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1aa8f70f-3161-4834-b019-55edb38b5ae4/dqc_reference/checkm_data
[2023-03-17 05:17:21,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:21,012] [INFO] Task started: CheckM
[2023-03-17 05:17:21,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7547/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7547/checkm_input OceanDNA-b7547/checkm_result
[2023-03-17 05:17:59,069] [INFO] Task succeeded: CheckM
[2023-03-17 05:17:59,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:17:59,073] [INFO] ===== Completeness check finished =====
[2023-03-17 05:17:59,073] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:17:59,073] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7547/markers.fasta)
[2023-03-17 05:17:59,075] [INFO] Task started: Blastn
[2023-03-17 05:17:59,075] [INFO] Running command: blastn -query OceanDNA-b7547/markers.fasta -db /var/lib/cwl/stg1aa8f70f-3161-4834-b019-55edb38b5ae4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7547/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:59,832] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:59,833] [INFO] Selected 10 target genomes.
[2023-03-17 05:17:59,833] [INFO] Target genome list was writen to OceanDNA-b7547/target_genomes_gtdb.txt
[2023-03-17 05:17:59,965] [INFO] Task started: fastANI
[2023-03-17 05:17:59,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgac682835-b987-4fc6-97a2-0670f20e09b0/OceanDNA-b7547.fa --refList OceanDNA-b7547/target_genomes_gtdb.txt --output OceanDNA-b7547/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:18:06,713] [INFO] Task succeeded: fastANI
[2023-03-17 05:18:06,719] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:18:06,719] [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_004195315.1	s__Lutibacter sp004195315	85.7414	383	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139515.1	s__Lutibacter sp013139515	82.1704	473	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041805.1	s__Lutibacter sp013041805	80.3956	476	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002733285.1	s__Lutibacter sp002733285	79.9285	412	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	97.79	97.79	0.89	0.89	2	-
GCA_016342705.1	s__Lutibacter sp016342705	79.8717	479	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	79.841	478	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188355.1	s__Lutibacter flavus	79.7282	501	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	79.2055	437	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004121075.1	s__Lutibacter sp004121075	78.97	391	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054895.1	s__Lutibacter sp018054895	78.4567	311	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:18:06,720] [INFO] GTDB search result was written to OceanDNA-b7547/result_gtdb.tsv
[2023-03-17 05:18:06,720] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:18:06,721] [INFO] DFAST_QC result json was written to OceanDNA-b7547/dqc_result.json
[2023-03-17 05:18:06,721] [INFO] DFAST_QC completed!
[2023-03-17 05:18:06,721] [INFO] Total running time: 0h1m9s