[2023-03-17 22:37:11,863] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:37:11,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:37:11,863] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaa56904-bf2c-4b15-a60a-1f29caeb4a96/dqc_reference
[2023-03-17 22:37:12,985] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:37:12,986] [INFO] Task started: Prodigal
[2023-03-17 22:37:12,986] [INFO] Running command: cat /var/lib/cwl/stg31b1e0f7-0c46-4afc-8743-60183baf4ace/OceanDNA-b11356.fa | prodigal -d OceanDNA-b11356/cds.fna -a OceanDNA-b11356/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:37:22,771] [INFO] Task succeeded: Prodigal
[2023-03-17 22:37:22,771] [INFO] Task started: HMMsearch
[2023-03-17 22:37:22,771] [INFO] Running command: hmmsearch --tblout OceanDNA-b11356/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaa56904-bf2c-4b15-a60a-1f29caeb4a96/dqc_reference/reference_markers.hmm OceanDNA-b11356/protein.faa > /dev/null
[2023-03-17 22:37:22,944] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:37:22,944] [INFO] Found 6/6 markers.
[2023-03-17 22:37:22,958] [INFO] Query marker FASTA was written to OceanDNA-b11356/markers.fasta
[2023-03-17 22:37:22,960] [INFO] Task started: Blastn
[2023-03-17 22:37:22,960] [INFO] Running command: blastn -query OceanDNA-b11356/markers.fasta -db /var/lib/cwl/stgfaa56904-bf2c-4b15-a60a-1f29caeb4a96/dqc_reference/reference_markers.fasta -out OceanDNA-b11356/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:23,608] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:23,608] [INFO] Selected 10 target genomes.
[2023-03-17 22:37:23,609] [INFO] Target genome list was writen to OceanDNA-b11356/target_genomes.txt
[2023-03-17 22:37:23,614] [INFO] Task started: fastANI
[2023-03-17 22:37:23,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg31b1e0f7-0c46-4afc-8743-60183baf4ace/OceanDNA-b11356.fa --refList OceanDNA-b11356/target_genomes.txt --output OceanDNA-b11356/fastani_result.tsv --threads 1
[2023-03-17 22:37:29,330] [INFO] Task succeeded: fastANI
[2023-03-17 22:37:29,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaa56904-bf2c-4b15-a60a-1f29caeb4a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:37:29,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaa56904-bf2c-4b15-a60a-1f29caeb4a96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:37:29,447] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-03-17 22:37:29,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 22:37:29,447] [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
Wenyingzhuangia marina	strain=DSM 100572	GCA_900130035.1	1195760	1195760	type	True	98.1279	445	471	95	conclusive
Wenyingzhuangia marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	98.0415	449	471	95	conclusive
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	85.1845	377	471	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	81.7877	301	471	95	below_threshold
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	81.5932	337	471	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.0767	126	471	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.035	100	471	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.7403	97	471	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.5135	110	471	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.4813	94	471	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:37:29,447] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11356/tc_result.tsv
[2023-03-17 22:37:29,447] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:37:29,447] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:37:29,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaa56904-bf2c-4b15-a60a-1f29caeb4a96/dqc_reference/checkm_data
[2023-03-17 22:37:29,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:37:29,451] [INFO] Task started: CheckM
[2023-03-17 22:37:29,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11356/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11356/checkm_input OceanDNA-b11356/checkm_result
[2023-03-17 22:37:59,446] [INFO] Task succeeded: CheckM
[2023-03-17 22:37:59,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 22:37:59,448] [INFO] ===== Completeness check finished =====
[2023-03-17 22:37:59,448] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:37:59,448] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11356/markers.fasta)
[2023-03-17 22:37:59,450] [INFO] Task started: Blastn
[2023-03-17 22:37:59,450] [INFO] Running command: blastn -query OceanDNA-b11356/markers.fasta -db /var/lib/cwl/stgfaa56904-bf2c-4b15-a60a-1f29caeb4a96/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11356/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:38:00,501] [INFO] Task succeeded: Blastn
[2023-03-17 22:38:00,502] [INFO] Selected 8 target genomes.
[2023-03-17 22:38:00,502] [INFO] Target genome list was writen to OceanDNA-b11356/target_genomes_gtdb.txt
[2023-03-17 22:38:00,561] [INFO] Task started: fastANI
[2023-03-17 22:38:00,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg31b1e0f7-0c46-4afc-8743-60183baf4ace/OceanDNA-b11356.fa --refList OceanDNA-b11356/target_genomes_gtdb.txt --output OceanDNA-b11356/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:38:05,128] [INFO] Task succeeded: fastANI
[2023-03-17 22:38:05,133] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 22:38:05,134] [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_900130035.1	s__Wenyingzhuangia marina	98.1279	445	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	85.1845	377	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762155.1	s__Wenyingzhuangia heitensis	81.7877	301	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927765.1	s__Wenyingzhuangia aestuarii	81.5859	337	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220525.1	s__Ochrovirga pacifica	78.7107	210	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ochrovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345825.1	s__Tenacibaculum skagerrakense	76.6428	77	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767245.1	s__Aureivirga sp015767245	76.2565	77	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	75.9693	50	471	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:38:05,134] [INFO] GTDB search result was written to OceanDNA-b11356/result_gtdb.tsv
[2023-03-17 22:38:05,134] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:38:05,135] [INFO] DFAST_QC result json was written to OceanDNA-b11356/dqc_result.json
[2023-03-17 22:38:05,135] [INFO] DFAST_QC completed!
[2023-03-17 22:38:05,135] [INFO] Total running time: 0h0m53s