[2023-03-18 01:54:18,004] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:54:18,004] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:54:18,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg52216a17-1d1b-4966-9d0c-e5834ed79caa/dqc_reference
[2023-03-18 01:54:19,093] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:54:19,093] [INFO] Task started: Prodigal
[2023-03-18 01:54:19,093] [INFO] Running command: cat /var/lib/cwl/stg26ce870d-0735-480c-847e-30e13e462e67/OceanDNA-b46216.fa | prodigal -d OceanDNA-b46216/cds.fna -a OceanDNA-b46216/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:54:29,110] [INFO] Task succeeded: Prodigal
[2023-03-18 01:54:29,110] [INFO] Task started: HMMsearch
[2023-03-18 01:54:29,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b46216/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52216a17-1d1b-4966-9d0c-e5834ed79caa/dqc_reference/reference_markers.hmm OceanDNA-b46216/protein.faa > /dev/null
[2023-03-18 01:54:29,255] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:54:29,255] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg26ce870d-0735-480c-847e-30e13e462e67/OceanDNA-b46216.fa]
[2023-03-18 01:54:29,268] [INFO] Query marker FASTA was written to OceanDNA-b46216/markers.fasta
[2023-03-18 01:54:29,268] [INFO] Task started: Blastn
[2023-03-18 01:54:29,268] [INFO] Running command: blastn -query OceanDNA-b46216/markers.fasta -db /var/lib/cwl/stg52216a17-1d1b-4966-9d0c-e5834ed79caa/dqc_reference/reference_markers.fasta -out OceanDNA-b46216/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:29,823] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:29,824] [INFO] Selected 27 target genomes.
[2023-03-18 01:54:29,824] [INFO] Target genome list was writen to OceanDNA-b46216/target_genomes.txt
[2023-03-18 01:54:29,837] [INFO] Task started: fastANI
[2023-03-18 01:54:29,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ce870d-0735-480c-847e-30e13e462e67/OceanDNA-b46216.fa --refList OceanDNA-b46216/target_genomes.txt --output OceanDNA-b46216/fastani_result.tsv --threads 1
[2023-03-18 01:54:47,389] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:47,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52216a17-1d1b-4966-9d0c-e5834ed79caa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:54:47,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52216a17-1d1b-4966-9d0c-e5834ed79caa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:54:47,390] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:54:47,390] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:54:47,390] [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 01:54:47,390] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46216/tc_result.tsv
[2023-03-18 01:54:47,390] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:54:47,390] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:54:47,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52216a17-1d1b-4966-9d0c-e5834ed79caa/dqc_reference/checkm_data
[2023-03-18 01:54:47,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:54:47,396] [INFO] Task started: CheckM
[2023-03-18 01:54:47,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46216/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46216/checkm_input OceanDNA-b46216/checkm_result
[2023-03-18 01:55:16,685] [INFO] Task succeeded: CheckM
[2023-03-18 01:55:16,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:55:16,687] [INFO] ===== Completeness check finished =====
[2023-03-18 01:55:16,687] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:55:16,687] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46216/markers.fasta)
[2023-03-18 01:55:16,688] [INFO] Task started: Blastn
[2023-03-18 01:55:16,688] [INFO] Running command: blastn -query OceanDNA-b46216/markers.fasta -db /var/lib/cwl/stg52216a17-1d1b-4966-9d0c-e5834ed79caa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46216/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:55:17,544] [INFO] Task succeeded: Blastn
[2023-03-18 01:55:17,545] [INFO] Selected 14 target genomes.
[2023-03-18 01:55:17,545] [INFO] Target genome list was writen to OceanDNA-b46216/target_genomes_gtdb.txt
[2023-03-18 01:55:17,562] [INFO] Task started: fastANI
[2023-03-18 01:55:17,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ce870d-0735-480c-847e-30e13e462e67/OceanDNA-b46216.fa --refList OceanDNA-b46216/target_genomes_gtdb.txt --output OceanDNA-b46216/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:55:22,234] [INFO] Task succeeded: fastANI
[2023-03-18 01:55:22,242] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:55:22,243] [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_002293125.1	s__UBA953 sp002293125	91.7849	210	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.83	99.83	0.93	0.93	2	-
GCA_003569165.1	s__UBA953 sp003569165	91.1102	201	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924535.1	s__UBA953 sp009924535	86.6979	152	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903910245.1	s__UBA953 sp903910245	86.3205	138	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831005.1	s__UBA953 sp903831005	86.2178	142	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853185.1	s__UBA953 sp903853185	86.1517	150	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	98.54	98.54	0.77	0.77	2	-
GCA_004293385.1	s__UBA953 sp004293385	85.9648	113	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921665.1	s__UBA953 sp903921665	85.8555	168	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917805.1	s__UBA953 sp009917805	85.8027	147	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913915.1	s__UBA953 sp903913915	85.6442	202	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.51	99.16	0.93	0.89	3	-
GCA_903855995.1	s__UBA953 sp903855995	82.7749	179	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.61	99.32	0.98	0.94	20	-
GCA_903829855.1	s__UBA953 sp903829855	81.8549	140	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.27	99.00	0.85	0.74	14	-
GCA_014193315.1	s__UBA953 sp003569405	81.8223	160	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.72	96.62	0.94	0.91	4	-
GCA_903882335.1	s__UBA953 sp903882335	81.8088	152	230	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	98.91	98.33	0.83	0.81	7	-
--------------------------------------------------------------------------------
[2023-03-18 01:55:22,243] [INFO] GTDB search result was written to OceanDNA-b46216/result_gtdb.tsv
[2023-03-18 01:55:22,243] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:55:22,244] [INFO] DFAST_QC result json was written to OceanDNA-b46216/dqc_result.json
[2023-03-18 01:55:22,244] [INFO] DFAST_QC completed!
[2023-03-18 01:55:22,244] [INFO] Total running time: 0h1m4s