[2023-03-18 07:54:29,689] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:29,689] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:29,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg80069155-1a44-4b6c-8aad-c1933e404d0d/dqc_reference
[2023-03-18 07:54:30,809] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:30,810] [INFO] Task started: Prodigal
[2023-03-18 07:54:30,810] [INFO] Running command: cat /var/lib/cwl/stg7da04482-d4c9-4724-a77e-12dc6cd58476/OceanDNA-b34265.fa | prodigal -d OceanDNA-b34265/cds.fna -a OceanDNA-b34265/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:58,953] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:58,953] [INFO] Task started: HMMsearch
[2023-03-18 07:54:58,953] [INFO] Running command: hmmsearch --tblout OceanDNA-b34265/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80069155-1a44-4b6c-8aad-c1933e404d0d/dqc_reference/reference_markers.hmm OceanDNA-b34265/protein.faa > /dev/null
[2023-03-18 07:54:59,206] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:59,207] [INFO] Found 6/6 markers.
[2023-03-18 07:54:59,235] [INFO] Query marker FASTA was written to OceanDNA-b34265/markers.fasta
[2023-03-18 07:54:59,236] [INFO] Task started: Blastn
[2023-03-18 07:54:59,236] [INFO] Running command: blastn -query OceanDNA-b34265/markers.fasta -db /var/lib/cwl/stg80069155-1a44-4b6c-8aad-c1933e404d0d/dqc_reference/reference_markers.fasta -out OceanDNA-b34265/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:00,143] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:00,144] [INFO] Selected 11 target genomes.
[2023-03-18 07:55:00,144] [INFO] Target genome list was writen to OceanDNA-b34265/target_genomes.txt
[2023-03-18 07:55:00,151] [INFO] Task started: fastANI
[2023-03-18 07:55:00,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg7da04482-d4c9-4724-a77e-12dc6cd58476/OceanDNA-b34265.fa --refList OceanDNA-b34265/target_genomes.txt --output OceanDNA-b34265/fastani_result.tsv --threads 1
[2023-03-18 07:55:11,053] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:11,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80069155-1a44-4b6c-8aad-c1933e404d0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:55:11,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80069155-1a44-4b6c-8aad-c1933e404d0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:55:11,061] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2023-03-18 07:55:11,061] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 07:55:11,061] [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
Aeromonas hydrophila	strain=ATCC 7966	GCA_001999685.1	644	644	type	True	96.9785	1321	1488	95	conclusive
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	96.9688	1371	1488	95	conclusive
Aeromonas hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	96.965	1378	1488	95	conclusive
Aeromonas hydrophila	strain=ATCC 7966	GCA_018360025.1	644	644	type	True	96.9644	1367	1488	95	conclusive
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	96.6668	1319	1488	95	conclusive
Aeromonas caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	88.8652	1161	1488	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.526	194	1488	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.4923	198	1488	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.3555	149	1488	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.2004	207	1488	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.1958	199	1488	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:55:11,062] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34265/tc_result.tsv
[2023-03-18 07:55:11,062] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:55:11,062] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:55:11,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80069155-1a44-4b6c-8aad-c1933e404d0d/dqc_reference/checkm_data
[2023-03-18 07:55:11,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:55:11,068] [INFO] Task started: CheckM
[2023-03-18 07:55:11,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34265/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34265/checkm_input OceanDNA-b34265/checkm_result
[2023-03-18 07:56:19,726] [INFO] Task succeeded: CheckM
[2023-03-18 07:56:19,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:56:19,730] [INFO] ===== Completeness check finished =====
[2023-03-18 07:56:19,730] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:56:19,730] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34265/markers.fasta)
[2023-03-18 07:56:19,731] [INFO] Task started: Blastn
[2023-03-18 07:56:19,731] [INFO] Running command: blastn -query OceanDNA-b34265/markers.fasta -db /var/lib/cwl/stg80069155-1a44-4b6c-8aad-c1933e404d0d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34265/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:56:21,332] [INFO] Task succeeded: Blastn
[2023-03-18 07:56:21,333] [INFO] Selected 14 target genomes.
[2023-03-18 07:56:21,333] [INFO] Target genome list was writen to OceanDNA-b34265/target_genomes_gtdb.txt
[2023-03-18 07:56:21,349] [INFO] Task started: fastANI
[2023-03-18 07:56:21,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg7da04482-d4c9-4724-a77e-12dc6cd58476/OceanDNA-b34265.fa --refList OceanDNA-b34265/target_genomes_gtdb.txt --output OceanDNA-b34265/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:56:35,950] [INFO] Task succeeded: fastANI
[2023-03-18 07:56:35,958] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:56:35,958] [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_000014805.1	s__Aeromonas hydrophila	96.9688	1371	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	conclusive
GCF_000820305.1	s__Aeromonas dhakensis	93.8047	1307	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000819745.1	s__Aeromonas bestiarum	90.3034	1282	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820085.1	s__Aeromonas sanarellii	89.0137	1105	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
GCF_000819785.1	s__Aeromonas caviae	88.8848	1127	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
GCF_000820165.1	s__Aeromonas taiwanensis	88.6797	1097	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	-
GCF_000819985.1	s__Aeromonas media	88.4405	1096	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_000819955.1	s__Aeromonas jandaei	87.7222	1158	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
GCF_000764665.1	s__Aeromonas lacus	87.6793	1130	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.97	96.97	0.94	0.94	2	-
GCF_000819845.1	s__Aeromonas enteropelogenes	87.6541	1112	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	-
GCF_019048265.1	s__Aeromonas veronii_A	87.6467	1170	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.07	95.82	0.91	0.90	4	-
GCF_000764645.1	s__Aeromonas finlandensis	87.5978	1027	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819885.1	s__Aeromonas fluvialis	87.1599	975	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819725.1	s__Aeromonas australiensis	87.0864	1016	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:56:35,958] [INFO] GTDB search result was written to OceanDNA-b34265/result_gtdb.tsv
[2023-03-18 07:56:35,959] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:56:35,960] [INFO] DFAST_QC result json was written to OceanDNA-b34265/dqc_result.json
[2023-03-18 07:56:35,960] [INFO] DFAST_QC completed!
[2023-03-18 07:56:35,960] [INFO] Total running time: 0h2m6s