[2023-03-19 04:11:06,927] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,927] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg17a730c5-925b-4ba1-a5b7-45284e084dee/dqc_reference
[2023-03-19 04:11:08,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,646] [INFO] Running command: cat /var/lib/cwl/stga71269f4-f10a-4298-a61e-f7db0de97a74/OceanDNA-b6778.fa | prodigal -d OceanDNA-b6778/cds.fna -a OceanDNA-b6778/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:29,090] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:29,090] [INFO] Task started: HMMsearch
[2023-03-19 04:11:29,090] [INFO] Running command: hmmsearch --tblout OceanDNA-b6778/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17a730c5-925b-4ba1-a5b7-45284e084dee/dqc_reference/reference_markers.hmm OceanDNA-b6778/protein.faa > /dev/null
[2023-03-19 04:11:29,295] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:29,296] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga71269f4-f10a-4298-a61e-f7db0de97a74/OceanDNA-b6778.fa]
[2023-03-19 04:11:29,317] [INFO] Query marker FASTA was written to OceanDNA-b6778/markers.fasta
[2023-03-19 04:11:29,318] [INFO] Task started: Blastn
[2023-03-19 04:11:29,318] [INFO] Running command: blastn -query OceanDNA-b6778/markers.fasta -db /var/lib/cwl/stg17a730c5-925b-4ba1-a5b7-45284e084dee/dqc_reference/reference_markers.fasta -out OceanDNA-b6778/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:29,902] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:29,903] [INFO] Selected 18 target genomes.
[2023-03-19 04:11:29,903] [INFO] Target genome list was writen to OceanDNA-b6778/target_genomes.txt
[2023-03-19 04:11:29,915] [INFO] Task started: fastANI
[2023-03-19 04:11:29,915] [INFO] Running command: fastANI --query /var/lib/cwl/stga71269f4-f10a-4298-a61e-f7db0de97a74/OceanDNA-b6778.fa --refList OceanDNA-b6778/target_genomes.txt --output OceanDNA-b6778/fastani_result.tsv --threads 1
[2023-03-19 04:11:42,794] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:42,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17a730c5-925b-4ba1-a5b7-45284e084dee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:42,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17a730c5-925b-4ba1-a5b7-45284e084dee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:42,806] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:42,806] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:42,806] [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
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	81.6662	609	1050	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	81.0968	610	1050	95	below_threshold
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	80.5794	586	1050	95	below_threshold
Flavobacterium frigoris	strain=DSM 15719	GCA_900111075.1	229204	229204	type	True	80.3036	549	1050	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	79.8451	515	1050	95	below_threshold
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	79.4575	413	1050	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	79.3214	482	1050	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	79.2789	453	1050	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	79.152	461	1050	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.1507	485	1050	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	79.0947	433	1050	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	78.4529	370	1050	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.3404	393	1050	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.586	319	1050	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.4149	252	1050	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.8934	61	1050	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	75.522	52	1050	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	75.492	83	1050	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:42,806] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6778/tc_result.tsv
[2023-03-19 04:11:42,806] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:42,806] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:42,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17a730c5-925b-4ba1-a5b7-45284e084dee/dqc_reference/checkm_data
[2023-03-19 04:11:42,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:42,834] [INFO] Task started: CheckM
[2023-03-19 04:11:42,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6778/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6778/checkm_input OceanDNA-b6778/checkm_result
[2023-03-19 04:12:34,785] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:34,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:34,788] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:34,788] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:34,789] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6778/markers.fasta)
[2023-03-19 04:12:34,789] [INFO] Task started: Blastn
[2023-03-19 04:12:34,789] [INFO] Running command: blastn -query OceanDNA-b6778/markers.fasta -db /var/lib/cwl/stg17a730c5-925b-4ba1-a5b7-45284e084dee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6778/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:35,651] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:35,652] [INFO] Selected 13 target genomes.
[2023-03-19 04:12:35,652] [INFO] Target genome list was writen to OceanDNA-b6778/target_genomes_gtdb.txt
[2023-03-19 04:12:35,671] [INFO] Task started: fastANI
[2023-03-19 04:12:35,671] [INFO] Running command: fastANI --query /var/lib/cwl/stga71269f4-f10a-4298-a61e-f7db0de97a74/OceanDNA-b6778.fa --refList OceanDNA-b6778/target_genomes_gtdb.txt --output OceanDNA-b6778/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:45,180] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:45,188] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:12:45,188] [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_014305155.1	s__Flavobacterium sp014305155	81.6611	610	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900106645.1	s__Flavobacterium degerlachei	81.1055	609	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252125.1	s__Flavobacterium frigoris_A	81.051	633	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107635.1	s__Flavobacterium gillisiae	80.5669	588	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294005.1	s__Flavobacterium sp013294005	80.0304	527	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.41	97.36	0.86	0.85	3	-
GCF_013294025.1	s__Flavobacterium sp013294025	79.4514	420	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425505.1	s__Flavobacterium frigidarium	79.439	415	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634755.1	s__Flavobacterium limicola	79.2733	455	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752255.1	s__Flavobacterium sp015752255	79.2078	480	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110375.1	s__Flavobacterium sinopsychrotolerans	79.1641	458	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995345.1	s__Flavobacterium sp017995345	79.1613	391	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.61	99.55	0.85	0.83	4	-
GCF_900108015.1	s__Flavobacterium urumqiense	79.1317	487	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097385.1	s__Flavobacterium sp007097385	78.5533	384	1050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:45,188] [INFO] GTDB search result was written to OceanDNA-b6778/result_gtdb.tsv
[2023-03-19 04:12:45,189] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:45,190] [INFO] DFAST_QC result json was written to OceanDNA-b6778/dqc_result.json
[2023-03-19 04:12:45,190] [INFO] DFAST_QC completed!
[2023-03-19 04:12:45,191] [INFO] Total running time: 0h1m38s