[2023-03-18 01:24:39,918] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:24:39,918] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:24:39,918] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5c292dd-3da2-4f78-8751-55df41877dd3/dqc_reference
[2023-03-18 01:24:41,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:24:41,193] [INFO] Task started: Prodigal
[2023-03-18 01:24:41,193] [INFO] Running command: cat /var/lib/cwl/stg4440b773-f037-44af-b81b-63ad88f62f18/OceanDNA-b8069.fa | prodigal -d OceanDNA-b8069/cds.fna -a OceanDNA-b8069/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:24:46,220] [INFO] Task succeeded: Prodigal
[2023-03-18 01:24:46,221] [INFO] Task started: HMMsearch
[2023-03-18 01:24:46,221] [INFO] Running command: hmmsearch --tblout OceanDNA-b8069/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5c292dd-3da2-4f78-8751-55df41877dd3/dqc_reference/reference_markers.hmm OceanDNA-b8069/protein.faa > /dev/null
[2023-03-18 01:24:46,394] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:24:46,394] [INFO] Found 6/6 markers.
[2023-03-18 01:24:46,402] [INFO] Query marker FASTA was written to OceanDNA-b8069/markers.fasta
[2023-03-18 01:24:46,403] [INFO] Task started: Blastn
[2023-03-18 01:24:46,403] [INFO] Running command: blastn -query OceanDNA-b8069/markers.fasta -db /var/lib/cwl/stgd5c292dd-3da2-4f78-8751-55df41877dd3/dqc_reference/reference_markers.fasta -out OceanDNA-b8069/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:24:47,132] [INFO] Task succeeded: Blastn
[2023-03-18 01:24:47,133] [INFO] Selected 31 target genomes.
[2023-03-18 01:24:47,133] [INFO] Target genome list was writen to OceanDNA-b8069/target_genomes.txt
[2023-03-18 01:24:47,142] [INFO] Task started: fastANI
[2023-03-18 01:24:47,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg4440b773-f037-44af-b81b-63ad88f62f18/OceanDNA-b8069.fa --refList OceanDNA-b8069/target_genomes.txt --output OceanDNA-b8069/fastani_result.tsv --threads 1
[2023-03-18 01:25:04,513] [INFO] Task succeeded: fastANI
[2023-03-18 01:25:04,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5c292dd-3da2-4f78-8751-55df41877dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:25:04,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5c292dd-3da2-4f78-8751-55df41877dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:25:04,514] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:25:04,514] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:25:04,514] [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
--------------------------------------------------------------------------------
[2023-03-18 01:25:04,514] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8069/tc_result.tsv
[2023-03-18 01:25:04,515] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:25:04,515] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:25:04,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5c292dd-3da2-4f78-8751-55df41877dd3/dqc_reference/checkm_data
[2023-03-18 01:25:04,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:25:04,520] [INFO] Task started: CheckM
[2023-03-18 01:25:04,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8069/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8069/checkm_input OceanDNA-b8069/checkm_result
[2023-03-18 01:25:22,852] [INFO] Task succeeded: CheckM
[2023-03-18 01:25:22,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:25:22,854] [INFO] ===== Completeness check finished =====
[2023-03-18 01:25:22,854] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:25:22,854] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8069/markers.fasta)
[2023-03-18 01:25:22,855] [INFO] Task started: Blastn
[2023-03-18 01:25:22,855] [INFO] Running command: blastn -query OceanDNA-b8069/markers.fasta -db /var/lib/cwl/stgd5c292dd-3da2-4f78-8751-55df41877dd3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8069/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:25:23,834] [INFO] Task succeeded: Blastn
[2023-03-18 01:25:23,835] [INFO] Selected 16 target genomes.
[2023-03-18 01:25:23,835] [INFO] Target genome list was writen to OceanDNA-b8069/target_genomes_gtdb.txt
[2023-03-18 01:25:23,900] [INFO] Task started: fastANI
[2023-03-18 01:25:23,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg4440b773-f037-44af-b81b-63ad88f62f18/OceanDNA-b8069.fa --refList OceanDNA-b8069/target_genomes_gtdb.txt --output OceanDNA-b8069/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:25:27,998] [INFO] Task succeeded: fastANI
[2023-03-18 01:25:28,008] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:25:28,008] [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_905181625.1	s__MAG-121220-bin8 sp905181625	93.5586	270	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	81.4166	189	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	78.3039	143	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	78.2028	129	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	78.0977	125	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	77.9904	107	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	77.9746	135	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510655.1	s__MAG-121220-bin8 sp902510655	77.9272	82	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	77.8316	96	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	77.7959	88	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	77.5951	77	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	77.5615	133	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780345.1	s__MAG-121220-bin8 sp016780345	77.3194	89	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.67	99.67	0.79	0.79	2	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	77.1179	107	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_004214185.1	s__MAG-121220-bin8 sp004214185	76.9946	88	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	-
--------------------------------------------------------------------------------
[2023-03-18 01:25:28,008] [INFO] GTDB search result was written to OceanDNA-b8069/result_gtdb.tsv
[2023-03-18 01:25:28,008] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:25:28,009] [INFO] DFAST_QC result json was written to OceanDNA-b8069/dqc_result.json
[2023-03-18 01:25:28,009] [INFO] DFAST_QC completed!
[2023-03-18 01:25:28,009] [INFO] Total running time: 0h0m48s