[2024-01-24 11:43:52,750] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:52,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:52,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7e4c32c-1661-4157-8d64-0639e8e3a0c6/dqc_reference
[2024-01-24 11:43:54,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,042] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,042] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e576402-74eb-474e-96a6-e992aee8aa61/GCF_000764645.1_ASM76464v1_genomic.fna.gz | prodigal -d GCF_000764645.1_ASM76464v1_genomic.fna/cds.fna -a GCF_000764645.1_ASM76464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:06,843] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:06,843] [INFO] Task started: HMMsearch
[2024-01-24 11:44:06,843] [INFO] Running command: hmmsearch --tblout GCF_000764645.1_ASM76464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7e4c32c-1661-4157-8d64-0639e8e3a0c6/dqc_reference/reference_markers.hmm GCF_000764645.1_ASM76464v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:07,071] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:07,072] [INFO] Found 6/6 markers.
[2024-01-24 11:44:07,110] [INFO] Query marker FASTA was written to GCF_000764645.1_ASM76464v1_genomic.fna/markers.fasta
[2024-01-24 11:44:07,110] [INFO] Task started: Blastn
[2024-01-24 11:44:07,110] [INFO] Running command: blastn -query GCF_000764645.1_ASM76464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7e4c32c-1661-4157-8d64-0639e8e3a0c6/dqc_reference/reference_markers.fasta -out GCF_000764645.1_ASM76464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:08,030] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:08,035] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:08,035] [INFO] Target genome list was writen to GCF_000764645.1_ASM76464v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:08,041] [INFO] Task started: fastANI
[2024-01-24 11:44:08,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e576402-74eb-474e-96a6-e992aee8aa61/GCF_000764645.1_ASM76464v1_genomic.fna.gz --refList GCF_000764645.1_ASM76464v1_genomic.fna/target_genomes.txt --output GCF_000764645.1_ASM76464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:21,630] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:21,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7e4c32c-1661-4157-8d64-0639e8e3a0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:21,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7e4c32c-1661-4157-8d64-0639e8e3a0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:21,644] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:21,644] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:21,644] [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 finlandensis	strain=4287D	GCA_000764645.1	1543375	1543375	type	True	99.9999	1376	1388	95	conclusive
Aeromonas veronii	strain=ATCC 35624	GCA_018359905.1	654	654	type	True	93.173	1167	1388	95	below_threshold
Aeromonas veronii	strain=CECT 4257	GCA_000820225.1	654	654	type	True	93.1056	1167	1388	95	below_threshold
Aeromonas allosaccharophila	strain=CECT 4199	GCA_000819685.1	656	656	type	True	93.0971	1140	1388	95	below_threshold
Aeromonas fluvialis	strain=LMG 24681	GCA_000819885.1	591962	591962	type	True	91.691	999	1388	95	below_threshold
Aeromonas australiensis	strain=CECT 8023	GCA_000819725.1	1114880	1114880	type	True	91.5561	1030	1388	95	below_threshold
Aeromonas lacus	strain=AE122	GCA_000764665.1	558884	558884	type	True	90.4797	1154	1388	95	below_threshold
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	87.6256	1096	1388	95	below_threshold
Aeromonas popoffii	strain=CIP 105493	GCA_000820025.1	70856	70856	type	True	87.2314	1060	1388	95	below_threshold
Aeromonas bestiarum	strain=CECT 4227	GCA_000819745.1	105751	105751	type	True	87.0671	1080	1388	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	77.0798	116	1388	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.7228	128	1388	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.6174	125	1388	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.4744	140	1388	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.463	133	1388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:21,646] [INFO] DFAST Taxonomy check result was written to GCF_000764645.1_ASM76464v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:21,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:21,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:21,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7e4c32c-1661-4157-8d64-0639e8e3a0c6/dqc_reference/checkm_data
[2024-01-24 11:44:21,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:21,694] [INFO] Task started: CheckM
[2024-01-24 11:44:21,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000764645.1_ASM76464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000764645.1_ASM76464v1_genomic.fna/checkm_input GCF_000764645.1_ASM76464v1_genomic.fna/checkm_result
[2024-01-24 11:45:00,747] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:00,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:00,766] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:00,766] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:00,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000764645.1_ASM76464v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:00,767] [INFO] Task started: Blastn
[2024-01-24 11:45:00,767] [INFO] Running command: blastn -query GCF_000764645.1_ASM76464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7e4c32c-1661-4157-8d64-0639e8e3a0c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000764645.1_ASM76464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:02,295] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:02,298] [INFO] Selected 11 target genomes.
[2024-01-24 11:45:02,298] [INFO] Target genome list was writen to GCF_000764645.1_ASM76464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:02,305] [INFO] Task started: fastANI
[2024-01-24 11:45:02,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e576402-74eb-474e-96a6-e992aee8aa61/GCF_000764645.1_ASM76464v1_genomic.fna.gz --refList GCF_000764645.1_ASM76464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000764645.1_ASM76464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:13,398] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:13,407] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:13,408] [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_000764645.1	s__Aeromonas finlandensis	99.9999	1376	1388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000820225.1	s__Aeromonas veronii	93.1056	1167	1388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.01	0.90	0.86	159	-
GCF_000819685.1	s__Aeromonas allosaccharophila	93.0971	1140	1388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.32	95.53	0.87	0.85	15	-
GCF_019048265.1	s__Aeromonas veronii_A	92.3579	1169	1388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.07	95.82	0.91	0.90	4	-
GCF_000819885.1	s__Aeromonas fluvialis	91.6954	998	1388	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	91.5532	1031	1388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204135.1	s__Aeromonas fluvialis_A	90.5628	1039	1388	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	90.4916	1153	1388	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	90.1651	1175	1388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
GCF_000014805.1	s__Aeromonas hydrophila	87.6285	1097	1388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_000820025.1	s__Aeromonas popoffii	87.2241	1060	1388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.17	98.00	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:13,409] [INFO] GTDB search result was written to GCF_000764645.1_ASM76464v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:13,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:13,413] [INFO] DFAST_QC result json was written to GCF_000764645.1_ASM76464v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:13,413] [INFO] DFAST_QC completed!
[2024-01-24 11:45:13,413] [INFO] Total running time: 0h1m21s