[2023-03-18 03:27:00,932] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,945] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dc92f39-012d-4610-86f3-971fc548ec5b/dqc_reference
[2023-03-18 03:27:02,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,640] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,640] [INFO] Running command: cat /var/lib/cwl/stg4dd6ad3e-37ee-4188-89a7-12c01ab28058/OceanDNA-b46662.fa | prodigal -d OceanDNA-b46662/cds.fna -a OceanDNA-b46662/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:34,073] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:34,073] [INFO] Task started: HMMsearch
[2023-03-18 03:27:34,073] [INFO] Running command: hmmsearch --tblout OceanDNA-b46662/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dc92f39-012d-4610-86f3-971fc548ec5b/dqc_reference/reference_markers.hmm OceanDNA-b46662/protein.faa > /dev/null
[2023-03-18 03:27:34,289] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:34,289] [INFO] Found 6/6 markers.
[2023-03-18 03:27:34,314] [INFO] Query marker FASTA was written to OceanDNA-b46662/markers.fasta
[2023-03-18 03:27:34,315] [INFO] Task started: Blastn
[2023-03-18 03:27:34,315] [INFO] Running command: blastn -query OceanDNA-b46662/markers.fasta -db /var/lib/cwl/stg7dc92f39-012d-4610-86f3-971fc548ec5b/dqc_reference/reference_markers.fasta -out OceanDNA-b46662/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:34,842] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:34,843] [INFO] Selected 23 target genomes.
[2023-03-18 03:27:34,843] [INFO] Target genome list was writen to OceanDNA-b46662/target_genomes.txt
[2023-03-18 03:27:34,857] [INFO] Task started: fastANI
[2023-03-18 03:27:34,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dd6ad3e-37ee-4188-89a7-12c01ab28058/OceanDNA-b46662.fa --refList OceanDNA-b46662/target_genomes.txt --output OceanDNA-b46662/fastani_result.tsv --threads 1
[2023-03-18 03:27:49,954] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:49,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dc92f39-012d-4610-86f3-971fc548ec5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:49,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dc92f39-012d-4610-86f3-971fc548ec5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:49,958] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:49,958] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:27:49,958] [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	76.1526	55	1250	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.0107	55	1250	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:27:49,958] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46662/tc_result.tsv
[2023-03-18 03:27:49,958] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:49,959] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:49,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dc92f39-012d-4610-86f3-971fc548ec5b/dqc_reference/checkm_data
[2023-03-18 03:27:49,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:50,106] [INFO] Task started: CheckM
[2023-03-18 03:27:50,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46662/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46662/checkm_input OceanDNA-b46662/checkm_result
[2023-03-18 03:29:08,164] [INFO] Task succeeded: CheckM
[2023-03-18 03:29:08,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:29:08,167] [INFO] ===== Completeness check finished =====
[2023-03-18 03:29:08,167] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:29:08,167] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46662/markers.fasta)
[2023-03-18 03:29:08,167] [INFO] Task started: Blastn
[2023-03-18 03:29:08,167] [INFO] Running command: blastn -query OceanDNA-b46662/markers.fasta -db /var/lib/cwl/stg7dc92f39-012d-4610-86f3-971fc548ec5b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46662/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:29:08,889] [INFO] Task succeeded: Blastn
[2023-03-18 03:29:08,890] [INFO] Selected 16 target genomes.
[2023-03-18 03:29:08,890] [INFO] Target genome list was writen to OceanDNA-b46662/target_genomes_gtdb.txt
[2023-03-18 03:29:08,907] [INFO] Task started: fastANI
[2023-03-18 03:29:08,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dd6ad3e-37ee-4188-89a7-12c01ab28058/OceanDNA-b46662.fa --refList OceanDNA-b46662/target_genomes_gtdb.txt --output OceanDNA-b46662/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:29:17,968] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:17,974] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:29:17,974] [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	99.3876	1205	1250	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905181965.1	s__SW10 sp905181965	81.8693	163	1250	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	78.2707	190	1250	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002323895.1	s__SW10 sp002323895	78.2501	104	1250	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	77.8191	146	1250	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	98.72	98.72	0.89	0.89	2	-
GCA_002420315.1	s__SW10 sp002420315	77.6619	90	1250	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.54	96.31	0.84	0.80	11	-
GCA_002729295.1	s__SW10 sp002729295	77.0595	142	1250	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.31	99.31	0.79	0.79	2	-
GCA_905478925.1	s__Luteolibacter sp905478925	76.6828	57	1250	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	97.95	97.95	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:29:17,974] [INFO] GTDB search result was written to OceanDNA-b46662/result_gtdb.tsv
[2023-03-18 03:29:17,974] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:29:17,975] [INFO] DFAST_QC result json was written to OceanDNA-b46662/dqc_result.json
[2023-03-18 03:29:17,975] [INFO] DFAST_QC completed!
[2023-03-18 03:29:17,975] [INFO] Total running time: 0h2m17s