[2023-03-16 10:01:01,814] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:01:01,814] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:01:01,814] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf81a912-2d53-42ca-ae02-d74a7c89d15f/dqc_reference
[2023-03-16 10:01:02,901] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:01:02,902] [INFO] Task started: Prodigal
[2023-03-16 10:01:02,902] [INFO] Running command: cat /var/lib/cwl/stga3807e1e-d040-47ee-9362-c617fec10392/OceanDNA-b45812.fa | prodigal -d OceanDNA-b45812/cds.fna -a OceanDNA-b45812/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:01:28,890] [INFO] Task succeeded: Prodigal
[2023-03-16 10:01:28,890] [INFO] Task started: HMMsearch
[2023-03-16 10:01:28,890] [INFO] Running command: hmmsearch --tblout OceanDNA-b45812/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf81a912-2d53-42ca-ae02-d74a7c89d15f/dqc_reference/reference_markers.hmm OceanDNA-b45812/protein.faa > /dev/null
[2023-03-16 10:01:29,084] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:01:29,084] [INFO] Found 6/6 markers.
[2023-03-16 10:01:29,105] [INFO] Query marker FASTA was written to OceanDNA-b45812/markers.fasta
[2023-03-16 10:01:29,106] [INFO] Task started: Blastn
[2023-03-16 10:01:29,106] [INFO] Running command: blastn -query OceanDNA-b45812/markers.fasta -db /var/lib/cwl/stgcf81a912-2d53-42ca-ae02-d74a7c89d15f/dqc_reference/reference_markers.fasta -out OceanDNA-b45812/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:01:29,754] [INFO] Task succeeded: Blastn
[2023-03-16 10:01:29,755] [INFO] Selected 14 target genomes.
[2023-03-16 10:01:29,755] [INFO] Target genome list was writen to OceanDNA-b45812/target_genomes.txt
[2023-03-16 10:01:29,765] [INFO] Task started: fastANI
[2023-03-16 10:01:29,766] [INFO] Running command: fastANI --query /var/lib/cwl/stga3807e1e-d040-47ee-9362-c617fec10392/OceanDNA-b45812.fa --refList OceanDNA-b45812/target_genomes.txt --output OceanDNA-b45812/fastani_result.tsv --threads 1
[2023-03-16 10:01:40,224] [INFO] Task succeeded: fastANI
[2023-03-16 10:01:40,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf81a912-2d53-42ca-ae02-d74a7c89d15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:01:40,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf81a912-2d53-42ca-ae02-d74a7c89d15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:01:40,230] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:01:40,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:01:40,230] [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
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.5931	59	914	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	76.5752	69	914	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	76.169	56	914	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.1679	68	914	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:01:40,231] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45812/tc_result.tsv
[2023-03-16 10:01:40,231] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:01:40,231] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:01:40,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf81a912-2d53-42ca-ae02-d74a7c89d15f/dqc_reference/checkm_data
[2023-03-16 10:01:40,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:01:40,239] [INFO] Task started: CheckM
[2023-03-16 10:01:40,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45812/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45812/checkm_input OceanDNA-b45812/checkm_result
[2023-03-16 10:02:46,626] [INFO] Task succeeded: CheckM
[2023-03-16 10:02:46,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:02:46,638] [INFO] ===== Completeness check finished =====
[2023-03-16 10:02:46,638] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:02:46,638] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45812/markers.fasta)
[2023-03-16 10:02:46,642] [INFO] Task started: Blastn
[2023-03-16 10:02:46,642] [INFO] Running command: blastn -query OceanDNA-b45812/markers.fasta -db /var/lib/cwl/stgcf81a912-2d53-42ca-ae02-d74a7c89d15f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45812/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:02:47,774] [INFO] Task succeeded: Blastn
[2023-03-16 10:02:47,775] [INFO] Selected 21 target genomes.
[2023-03-16 10:02:47,775] [INFO] Target genome list was writen to OceanDNA-b45812/target_genomes_gtdb.txt
[2023-03-16 10:02:47,792] [INFO] Task started: fastANI
[2023-03-16 10:02:47,793] [INFO] Running command: fastANI --query /var/lib/cwl/stga3807e1e-d040-47ee-9362-c617fec10392/OceanDNA-b45812.fa --refList OceanDNA-b45812/target_genomes_gtdb.txt --output OceanDNA-b45812/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:03:00,717] [INFO] Task succeeded: fastANI
[2023-03-16 10:03:00,725] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:03:00,725] [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_002367815.1	s__Cephaloticoccus sp002367815	99.629	770	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Cephaloticoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002713695.1	s__Cephaloticoccus sp002713695	77.1186	130	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Cephaloticoccus	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002344205.1	s__UBA2377 sp002344205	76.6023	123	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	99.84	99.84	0.94	0.94	2	-
GCA_016794785.1	s__ER46 sp016794785	76.591	65	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239845.1	s__Opitutus sp018239845	76.5872	87	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881475.1	s__Opi-474 sp903881475	76.5101	68	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.50	98.31	0.92	0.83	9	-
GCA_002288455.1	s__ER46 sp002288455	76.4685	59	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903820035.1	s__ER46 sp903820035	76.35	65	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.61	99.58	0.90	0.89	3	-
GCA_903859715.1	s__Opi-474 sp903859715	76.281	81	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.98	99.96	0.98	0.96	7	-
GCF_000019965.1	s__Opitutus terrae	76.1679	68	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209255.1	s__ER46 sp016209255	76.1224	55	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304445.1	s__Tous-C4FEB sp002304445	76.1209	67	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	98.22	97.15	0.85	0.81	4	-
GCA_903925425.1	s__CAIYFD01 sp903925425	76.0143	51	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIYFD01	95.0	98.64	98.42	0.84	0.82	3	-
--------------------------------------------------------------------------------
[2023-03-16 10:03:00,727] [INFO] GTDB search result was written to OceanDNA-b45812/result_gtdb.tsv
[2023-03-16 10:03:00,727] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:03:00,730] [INFO] DFAST_QC result json was written to OceanDNA-b45812/dqc_result.json
[2023-03-16 10:03:00,730] [INFO] DFAST_QC completed!
[2023-03-16 10:03:00,730] [INFO] Total running time: 0h1m59s