[2023-03-17 02:18:54,393] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:18:54,393] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:18:54,393] [INFO] DQC Reference Directory: /var/lib/cwl/stg56dd68a1-c270-4400-8998-a9f9f6051de4/dqc_reference
[2023-03-17 02:18:56,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:18:56,729] [INFO] Task started: Prodigal
[2023-03-17 02:18:56,729] [INFO] Running command: cat /var/lib/cwl/stg60159182-0064-4268-ba8f-9a97c855d9f1/OceanDNA-b46812.fa | prodigal -d OceanDNA-b46812/cds.fna -a OceanDNA-b46812/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:19:34,417] [INFO] Task succeeded: Prodigal
[2023-03-17 02:19:34,417] [INFO] Task started: HMMsearch
[2023-03-17 02:19:34,417] [INFO] Running command: hmmsearch --tblout OceanDNA-b46812/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56dd68a1-c270-4400-8998-a9f9f6051de4/dqc_reference/reference_markers.hmm OceanDNA-b46812/protein.faa > /dev/null
[2023-03-17 02:19:34,634] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:19:34,634] [INFO] Found 6/6 markers.
[2023-03-17 02:19:34,660] [INFO] Query marker FASTA was written to OceanDNA-b46812/markers.fasta
[2023-03-17 02:19:34,660] [INFO] Task started: Blastn
[2023-03-17 02:19:34,660] [INFO] Running command: blastn -query OceanDNA-b46812/markers.fasta -db /var/lib/cwl/stg56dd68a1-c270-4400-8998-a9f9f6051de4/dqc_reference/reference_markers.fasta -out OceanDNA-b46812/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:19:35,175] [INFO] Task succeeded: Blastn
[2023-03-17 02:19:35,176] [INFO] Selected 23 target genomes.
[2023-03-17 02:19:35,176] [INFO] Target genome list was writen to OceanDNA-b46812/target_genomes.txt
[2023-03-17 02:19:35,189] [INFO] Task started: fastANI
[2023-03-17 02:19:35,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg60159182-0064-4268-ba8f-9a97c855d9f1/OceanDNA-b46812.fa --refList OceanDNA-b46812/target_genomes.txt --output OceanDNA-b46812/fastani_result.tsv --threads 1
[2023-03-17 02:19:52,099] [INFO] Task succeeded: fastANI
[2023-03-17 02:19:52,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56dd68a1-c270-4400-8998-a9f9f6051de4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:19:52,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56dd68a1-c270-4400-8998-a9f9f6051de4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:19:52,105] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:19:52,105] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:19:52,105] [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
Roseibacillus persicicus	strain=KCTC 12988	GCA_014651675.1	454148	454148	type	True	76.6844	56	1475	95	below_threshold
Roseibacillus ishigakijimensis	strain=KCTC 12986	GCA_016595415.1	454146	454146	type	True	76.3318	63	1475	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.2781	52	1475	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:19:52,105] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46812/tc_result.tsv
[2023-03-17 02:19:52,105] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:19:52,105] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:19:52,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56dd68a1-c270-4400-8998-a9f9f6051de4/dqc_reference/checkm_data
[2023-03-17 02:19:52,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:19:52,112] [INFO] Task started: CheckM
[2023-03-17 02:19:52,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46812/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46812/checkm_input OceanDNA-b46812/checkm_result
[2023-03-17 02:21:24,080] [INFO] Task succeeded: CheckM
[2023-03-17 02:21:24,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:21:24,084] [INFO] ===== Completeness check finished =====
[2023-03-17 02:21:24,084] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:21:24,084] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46812/markers.fasta)
[2023-03-17 02:21:24,086] [INFO] Task started: Blastn
[2023-03-17 02:21:24,086] [INFO] Running command: blastn -query OceanDNA-b46812/markers.fasta -db /var/lib/cwl/stg56dd68a1-c270-4400-8998-a9f9f6051de4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46812/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:21:24,817] [INFO] Task succeeded: Blastn
[2023-03-17 02:21:24,818] [INFO] Selected 22 target genomes.
[2023-03-17 02:21:24,818] [INFO] Target genome list was writen to OceanDNA-b46812/target_genomes_gtdb.txt
[2023-03-17 02:21:25,580] [INFO] Task started: fastANI
[2023-03-17 02:21:25,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg60159182-0064-4268-ba8f-9a97c855d9f1/OceanDNA-b46812.fa --refList OceanDNA-b46812/target_genomes_gtdb.txt --output OceanDNA-b46812/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:21:43,025] [INFO] Task succeeded: fastANI
[2023-03-17 02:21:43,030] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:21:43,030] [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_905182405.1	s__SW10 sp905182405	82.0405	376	1475	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181965.1	s__SW10 sp905181965	78.8742	179	1475	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.78	97.70	0.75	0.63	5	-
GCA_018222765.1	s__SW10 sp018222765	78.1476	243	1475	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420315.1	s__SW10 sp002420315	78.1474	210	1475	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.54	96.31	0.84	0.80	11	-
GCA_002323895.1	s__SW10 sp002323895	78.1126	223	1475	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.17	98.66	0.86	0.81	3	-
GCA_002172625.1	s__SW10 sp002172625	77.8558	194	1475	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	98.72	98.72	0.89	0.89	2	-
GCA_002729295.1	s__SW10 sp002729295	77.7405	169	1475	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.31	99.31	0.79	0.79	2	-
GCF_014904755.1	s__Haloferula sp014904755	75.7719	58	1475	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:21:43,031] [INFO] GTDB search result was written to OceanDNA-b46812/result_gtdb.tsv
[2023-03-17 02:21:43,031] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:21:43,032] [INFO] DFAST_QC result json was written to OceanDNA-b46812/dqc_result.json
[2023-03-17 02:21:43,032] [INFO] DFAST_QC completed!
[2023-03-17 02:21:43,032] [INFO] Total running time: 0h2m49s