[2024-01-24 12:14:35,856] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa68cbf3-3cfb-4b6a-a7e8-06c520cbf0af/dqc_reference
[2024-01-24 12:14:37,191] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:37,192] [INFO] Task started: Prodigal
[2024-01-24 12:14:37,192] [INFO] Running command: gunzip -c /var/lib/cwl/stg3726da46-956f-4a84-914f-2df9296e23ce/GCF_900476005.1_51438_H01_genomic.fna.gz | prodigal -d GCF_900476005.1_51438_H01_genomic.fna/cds.fna -a GCF_900476005.1_51438_H01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:54,868] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:54,868] [INFO] Task started: HMMsearch
[2024-01-24 12:14:54,868] [INFO] Running command: hmmsearch --tblout GCF_900476005.1_51438_H01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa68cbf3-3cfb-4b6a-a7e8-06c520cbf0af/dqc_reference/reference_markers.hmm GCF_900476005.1_51438_H01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:55,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:55,134] [INFO] Found 6/6 markers.
[2024-01-24 12:14:55,174] [INFO] Query marker FASTA was written to GCF_900476005.1_51438_H01_genomic.fna/markers.fasta
[2024-01-24 12:14:55,174] [INFO] Task started: Blastn
[2024-01-24 12:14:55,174] [INFO] Running command: blastn -query GCF_900476005.1_51438_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa68cbf3-3cfb-4b6a-a7e8-06c520cbf0af/dqc_reference/reference_markers.fasta -out GCF_900476005.1_51438_H01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:56,164] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:56,168] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:56,168] [INFO] Target genome list was writen to GCF_900476005.1_51438_H01_genomic.fna/target_genomes.txt
[2024-01-24 12:14:56,173] [INFO] Task started: fastANI
[2024-01-24 12:14:56,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg3726da46-956f-4a84-914f-2df9296e23ce/GCF_900476005.1_51438_H01_genomic.fna.gz --refList GCF_900476005.1_51438_H01_genomic.fna/target_genomes.txt --output GCF_900476005.1_51438_H01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:10,233] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:10,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa68cbf3-3cfb-4b6a-a7e8-06c520cbf0af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:10,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa68cbf3-3cfb-4b6a-a7e8-06c520cbf0af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:10,248] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:15:10,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:10,248] [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 caviae	strain=NCTC12244	GCA_900476005.1	648	648	type	True	100.0	1524	1528	95	conclusive
Aeromonas caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	99.9876	1470	1528	95	conclusive
Aeromonas caviae	strain=CECT 838	GCA_000819785.1	648	648	type	True	99.9388	1436	1528	95	conclusive
Aeromonas taiwanensis	strain=LMG 24683	GCA_000820165.1	633417	633417	type	True	91.0157	1196	1528	95	below_threshold
Aeromonas taiwanensis	strain=LMG 24683	GCA_000699185.1	633417	633417	type	True	90.9364	1204	1528	95	below_threshold
Aeromonas hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	89.0579	1233	1528	95	below_threshold
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	89.0532	1242	1528	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	89.0211	1184	1528	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	88.9353	1174	1528	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	77.2767	254	1528	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.6638	137	1528	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.6537	176	1528	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.6312	144	1528	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2367	109	1528	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:10,250] [INFO] DFAST Taxonomy check result was written to GCF_900476005.1_51438_H01_genomic.fna/tc_result.tsv
[2024-01-24 12:15:10,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:10,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:10,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa68cbf3-3cfb-4b6a-a7e8-06c520cbf0af/dqc_reference/checkm_data
[2024-01-24 12:15:10,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:10,299] [INFO] Task started: CheckM
[2024-01-24 12:15:10,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900476005.1_51438_H01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900476005.1_51438_H01_genomic.fna/checkm_input GCF_900476005.1_51438_H01_genomic.fna/checkm_result
[2024-01-24 12:16:01,209] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:01,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:01,228] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:01,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:01,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900476005.1_51438_H01_genomic.fna/markers.fasta)
[2024-01-24 12:16:01,229] [INFO] Task started: Blastn
[2024-01-24 12:16:01,230] [INFO] Running command: blastn -query GCF_900476005.1_51438_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa68cbf3-3cfb-4b6a-a7e8-06c520cbf0af/dqc_reference/reference_markers_gtdb.fasta -out GCF_900476005.1_51438_H01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:02,805] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:02,809] [INFO] Selected 10 target genomes.
[2024-01-24 12:16:02,809] [INFO] Target genome list was writen to GCF_900476005.1_51438_H01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:02,814] [INFO] Task started: fastANI
[2024-01-24 12:16:02,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg3726da46-956f-4a84-914f-2df9296e23ce/GCF_900476005.1_51438_H01_genomic.fna.gz --refList GCF_900476005.1_51438_H01_genomic.fna/target_genomes_gtdb.txt --output GCF_900476005.1_51438_H01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:13,875] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:13,884] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:13,884] [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_000819785.1	s__Aeromonas caviae	99.9388	1436	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	conclusive
GCF_000820085.1	s__Aeromonas sanarellii	91.6213	1219	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
GCF_000820165.1	s__Aeromonas taiwanensis	91.0183	1196	1528	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	89.9368	1199	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_000014805.1	s__Aeromonas hydrophila	89.0514	1242	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_000820305.1	s__Aeromonas dhakensis	89.0168	1184	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000819845.1	s__Aeromonas enteropelogenes	86.5633	1095	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	-
GCF_014204135.1	s__Aeromonas fluvialis_A	86.0123	1001	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764665.1	s__Aeromonas lacus	85.9322	1072	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.97	96.97	0.94	0.94	2	-
GCF_000819955.1	s__Aeromonas jandaei	85.9298	1081	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:13,886] [INFO] GTDB search result was written to GCF_900476005.1_51438_H01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:13,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:13,891] [INFO] DFAST_QC result json was written to GCF_900476005.1_51438_H01_genomic.fna/dqc_result.json
[2024-01-24 12:16:13,892] [INFO] DFAST_QC completed!
[2024-01-24 12:16:13,892] [INFO] Total running time: 0h1m38s