[2024-01-24 12:21:59,277] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:59,279] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:59,279] [INFO] DQC Reference Directory: /var/lib/cwl/stg30d3ebdc-71be-4d04-a1b3-638a2aaf77ff/dqc_reference
[2024-01-24 12:22:00,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:00,791] [INFO] Task started: Prodigal
[2024-01-24 12:22:00,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg335e42f7-3e8b-460f-a357-ae6fab548437/GCF_001908535.1_ASM190853v1_genomic.fna.gz | prodigal -d GCF_001908535.1_ASM190853v1_genomic.fna/cds.fna -a GCF_001908535.1_ASM190853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:15,023] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:15,023] [INFO] Task started: HMMsearch
[2024-01-24 12:22:15,023] [INFO] Running command: hmmsearch --tblout GCF_001908535.1_ASM190853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30d3ebdc-71be-4d04-a1b3-638a2aaf77ff/dqc_reference/reference_markers.hmm GCF_001908535.1_ASM190853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:15,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:15,364] [INFO] Found 6/6 markers.
[2024-01-24 12:22:15,401] [INFO] Query marker FASTA was written to GCF_001908535.1_ASM190853v1_genomic.fna/markers.fasta
[2024-01-24 12:22:15,402] [INFO] Task started: Blastn
[2024-01-24 12:22:15,402] [INFO] Running command: blastn -query GCF_001908535.1_ASM190853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30d3ebdc-71be-4d04-a1b3-638a2aaf77ff/dqc_reference/reference_markers.fasta -out GCF_001908535.1_ASM190853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:16,406] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:16,409] [INFO] Selected 14 target genomes.
[2024-01-24 12:22:16,409] [INFO] Target genome list was writen to GCF_001908535.1_ASM190853v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:16,422] [INFO] Task started: fastANI
[2024-01-24 12:22:16,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg335e42f7-3e8b-460f-a357-ae6fab548437/GCF_001908535.1_ASM190853v1_genomic.fna.gz --refList GCF_001908535.1_ASM190853v1_genomic.fna/target_genomes.txt --output GCF_001908535.1_ASM190853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:30,277] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:30,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30d3ebdc-71be-4d04-a1b3-638a2aaf77ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:30,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30d3ebdc-71be-4d04-a1b3-638a2aaf77ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:30,291] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:30,291] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:30,291] [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 veronii	strain=ATCC 35624	GCA_018359905.1	654	654	type	True	99.9871	1467	1484	95	conclusive
Aeromonas veronii	strain=CECT 4257	GCA_000820225.1	654	654	type	True	99.9737	1458	1484	95	conclusive
Aeromonas allosaccharophila	strain=CECT 4199	GCA_000819685.1	656	656	type	True	94.0943	1231	1484	95	below_threshold
Aeromonas australiensis	strain=CECT 8023	GCA_000819725.1	1114880	1114880	type	True	93.2572	1152	1484	95	below_threshold
Aeromonas finlandensis	strain=4287D	GCA_000764645.1	1543375	1543375	type	True	93.1101	1146	1484	95	below_threshold
Aeromonas fluvialis	strain=LMG 24681	GCA_000819885.1	591962	591962	type	True	92.5776	1094	1484	95	below_threshold
Aeromonas lacus	strain=AE122	GCA_000764665.1	558884	558884	type	True	90.8434	1193	1484	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_986	GCA_016127195.1	650	650	type	True	90.676	1267	1484	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	87.5772	1167	1484	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.6168	140	1484	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	76.5605	97	1484	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.4779	96	1484	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.2316	108	1484	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	75.8765	80	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:30,297] [INFO] DFAST Taxonomy check result was written to GCF_001908535.1_ASM190853v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:30,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:30,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:30,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30d3ebdc-71be-4d04-a1b3-638a2aaf77ff/dqc_reference/checkm_data
[2024-01-24 12:22:30,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:30,359] [INFO] Task started: CheckM
[2024-01-24 12:22:30,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001908535.1_ASM190853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001908535.1_ASM190853v1_genomic.fna/checkm_input GCF_001908535.1_ASM190853v1_genomic.fna/checkm_result
[2024-01-24 12:23:13,631] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:13,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:13,651] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:13,651] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:13,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001908535.1_ASM190853v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:13,652] [INFO] Task started: Blastn
[2024-01-24 12:23:13,652] [INFO] Running command: blastn -query GCF_001908535.1_ASM190853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30d3ebdc-71be-4d04-a1b3-638a2aaf77ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_001908535.1_ASM190853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:15,216] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:15,219] [INFO] Selected 10 target genomes.
[2024-01-24 12:23:15,219] [INFO] Target genome list was writen to GCF_001908535.1_ASM190853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:15,226] [INFO] Task started: fastANI
[2024-01-24 12:23:15,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg335e42f7-3e8b-460f-a357-ae6fab548437/GCF_001908535.1_ASM190853v1_genomic.fna.gz --refList GCF_001908535.1_ASM190853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001908535.1_ASM190853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:25,919] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:25,935] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:25,935] [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_000820225.1	s__Aeromonas veronii	99.9737	1458	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.01	0.90	0.86	159	conclusive
GCF_019048265.1	s__Aeromonas veronii_A	94.8444	1278	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.07	95.82	0.91	0.90	4	-
GCF_000819685.1	s__Aeromonas allosaccharophila	94.0943	1231	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.32	95.53	0.87	0.85	15	-
GCF_000819725.1	s__Aeromonas australiensis	93.2508	1153	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764645.1	s__Aeromonas finlandensis	93.1075	1146	1484	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	92.5776	1094	1484	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	90.8434	1193	1484	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	90.6999	1251	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
GCF_014204135.1	s__Aeromonas fluvialis_A	90.5746	1109	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820305.1	s__Aeromonas dhakensis	87.576	1167	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:25,937] [INFO] GTDB search result was written to GCF_001908535.1_ASM190853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:25,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:25,943] [INFO] DFAST_QC result json was written to GCF_001908535.1_ASM190853v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:25,943] [INFO] DFAST_QC completed!
[2024-01-24 12:23:25,943] [INFO] Total running time: 0h1m27s