[2024-01-24 13:40:28,528] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg80f44358-f519-4435-9f14-8c2d9413be33/dqc_reference
[2024-01-24 13:40:31,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,145] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg25a056c0-185f-4800-ac24-ffd948021788/GCF_002795305.1_ASM279530v1_genomic.fna.gz | prodigal -d GCF_002795305.1_ASM279530v1_genomic.fna/cds.fna -a GCF_002795305.1_ASM279530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:41,413] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:41,414] [INFO] Task started: HMMsearch
[2024-01-24 13:40:41,414] [INFO] Running command: hmmsearch --tblout GCF_002795305.1_ASM279530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80f44358-f519-4435-9f14-8c2d9413be33/dqc_reference/reference_markers.hmm GCF_002795305.1_ASM279530v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:41,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:41,738] [INFO] Found 6/6 markers.
[2024-01-24 13:40:41,773] [INFO] Query marker FASTA was written to GCF_002795305.1_ASM279530v1_genomic.fna/markers.fasta
[2024-01-24 13:40:41,774] [INFO] Task started: Blastn
[2024-01-24 13:40:41,774] [INFO] Running command: blastn -query GCF_002795305.1_ASM279530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80f44358-f519-4435-9f14-8c2d9413be33/dqc_reference/reference_markers.fasta -out GCF_002795305.1_ASM279530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:42,700] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:42,709] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:42,710] [INFO] Target genome list was writen to GCF_002795305.1_ASM279530v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:42,740] [INFO] Task started: fastANI
[2024-01-24 13:40:42,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg25a056c0-185f-4800-ac24-ffd948021788/GCF_002795305.1_ASM279530v1_genomic.fna.gz --refList GCF_002795305.1_ASM279530v1_genomic.fna/target_genomes.txt --output GCF_002795305.1_ASM279530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:56,599] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:56,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80f44358-f519-4435-9f14-8c2d9413be33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:56,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80f44358-f519-4435-9f14-8c2d9413be33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:56,617] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:56,617] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:56,618] [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 cavernicola	strain=DSM 24474	GCA_002795305.1	1006623	1006623	type	True	100.0	1151	1157	95	conclusive
Aeromonas veronii	strain=CECT 4257	GCA_000820225.1	654	654	type	True	84.4108	685	1157	95	below_threshold
Aeromonas veronii	strain=ATCC 35624	GCA_018359905.1	654	654	type	True	84.3692	692	1157	95	below_threshold
Aeromonas allosaccharophila	strain=CECT 4199	GCA_000819685.1	656	656	type	True	84.3201	691	1157	95	below_threshold
Aeromonas finlandensis	strain=4287D	GCA_000764645.1	1543375	1543375	type	True	84.0374	672	1157	95	below_threshold
Aeromonas australiensis	strain=CECT 8023	GCA_000819725.1	1114880	1114880	type	True	83.6422	663	1157	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_986	GCA_016127195.1	650	650	type	True	83.563	677	1157	95	below_threshold
Aeromonas lacus	strain=AE122	GCA_000764665.1	558884	558884	type	True	83.5083	686	1157	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	82.8115	648	1157	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	82.6102	656	1157	95	below_threshold
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	82.5918	688	1157	95	below_threshold
Aeromonas hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	82.5852	683	1157	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.7482	88	1157	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.4192	61	1157	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.4096	60	1157	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.3172	67	1157	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.2401	65	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:56,619] [INFO] DFAST Taxonomy check result was written to GCF_002795305.1_ASM279530v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:56,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:56,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:56,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80f44358-f519-4435-9f14-8c2d9413be33/dqc_reference/checkm_data
[2024-01-24 13:40:56,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:56,671] [INFO] Task started: CheckM
[2024-01-24 13:40:56,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002795305.1_ASM279530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002795305.1_ASM279530v1_genomic.fna/checkm_input GCF_002795305.1_ASM279530v1_genomic.fna/checkm_result
[2024-01-24 13:41:32,693] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:32,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:32,719] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:32,720] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:32,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002795305.1_ASM279530v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:32,721] [INFO] Task started: Blastn
[2024-01-24 13:41:32,721] [INFO] Running command: blastn -query GCF_002795305.1_ASM279530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80f44358-f519-4435-9f14-8c2d9413be33/dqc_reference/reference_markers_gtdb.fasta -out GCF_002795305.1_ASM279530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:34,119] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:34,123] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:34,123] [INFO] Target genome list was writen to GCF_002795305.1_ASM279530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:34,142] [INFO] Task started: fastANI
[2024-01-24 13:41:34,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg25a056c0-185f-4800-ac24-ffd948021788/GCF_002795305.1_ASM279530v1_genomic.fna.gz --refList GCF_002795305.1_ASM279530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002795305.1_ASM279530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:45,621] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:45,637] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:45,637] [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_002795305.1	s__Aeromonas cavernicola	100.0	1151	1157	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	84.438	683	1157	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	84.3269	690	1157	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	84.0407	694	1157	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	84.0313	671	1157	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	83.8644	653	1157	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	83.6734	648	1157	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	83.6281	664	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819955.1	s__Aeromonas jandaei	83.5364	669	1157	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	83.4951	687	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.97	96.97	0.94	0.94	2	-
GCF_000820305.1	s__Aeromonas dhakensis	82.5932	656	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000014805.1	s__Aeromonas hydrophila	82.5708	689	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_900637545.1	s__Aeromonas encheleia	81.7431	609	1157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,639] [INFO] GTDB search result was written to GCF_002795305.1_ASM279530v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:45,646] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:45,654] [INFO] DFAST_QC result json was written to GCF_002795305.1_ASM279530v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:45,655] [INFO] DFAST_QC completed!
[2024-01-24 13:41:45,655] [INFO] Total running time: 0h1m17s