[2024-01-24 11:34:39,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:39,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:39,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg505e2ed2-445d-4c79-a122-be3d9756b7d4/dqc_reference
[2024-01-24 11:34:40,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:40,480] [INFO] Task started: Prodigal
[2024-01-24 11:34:40,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg47a3e228-d189-4e04-9ef7-b95c41d1c737/GCF_020341535.1_ASM2034153v1_genomic.fna.gz | prodigal -d GCF_020341535.1_ASM2034153v1_genomic.fna/cds.fna -a GCF_020341535.1_ASM2034153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:54,530] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:54,530] [INFO] Task started: HMMsearch
[2024-01-24 11:34:54,530] [INFO] Running command: hmmsearch --tblout GCF_020341535.1_ASM2034153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg505e2ed2-445d-4c79-a122-be3d9756b7d4/dqc_reference/reference_markers.hmm GCF_020341535.1_ASM2034153v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:54,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:54,863] [INFO] Found 6/6 markers.
[2024-01-24 11:34:54,918] [INFO] Query marker FASTA was written to GCF_020341535.1_ASM2034153v1_genomic.fna/markers.fasta
[2024-01-24 11:34:54,918] [INFO] Task started: Blastn
[2024-01-24 11:34:54,918] [INFO] Running command: blastn -query GCF_020341535.1_ASM2034153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg505e2ed2-445d-4c79-a122-be3d9756b7d4/dqc_reference/reference_markers.fasta -out GCF_020341535.1_ASM2034153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:55,874] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:55,878] [INFO] Selected 13 target genomes.
[2024-01-24 11:34:55,878] [INFO] Target genome list was writen to GCF_020341535.1_ASM2034153v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:55,884] [INFO] Task started: fastANI
[2024-01-24 11:34:55,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg47a3e228-d189-4e04-9ef7-b95c41d1c737/GCF_020341535.1_ASM2034153v1_genomic.fna.gz --refList GCF_020341535.1_ASM2034153v1_genomic.fna/target_genomes.txt --output GCF_020341535.1_ASM2034153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:09,345] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:09,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg505e2ed2-445d-4c79-a122-be3d9756b7d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:09,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg505e2ed2-445d-4c79-a122-be3d9756b7d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:09,358] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:35:09,358] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:09,359] [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 jandaei	strain=FDAARGOS_1523	GCA_020341535.1	650	650	type	True	100.0	1513	1515	95	inconclusive
Aeromonas jandaei	strain=FDAARGOS_986	GCA_016127195.1	650	650	type	True	99.9994	1512	1515	95	inconclusive
Aeromonas jandaei	strain=CECT 4228	GCA_000819955.1	650	650	type	True	99.946	1467	1515	95	inconclusive
Aeromonas lacus	strain=AE122	GCA_000764665.1	558884	558884	type	True	95.7751	1323	1515	95	inconclusive
Aeromonas allosaccharophila	strain=CECT 4199	GCA_000819685.1	656	656	type	True	90.1672	1187	1515	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	87.9659	1174	1515	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	87.6523	1216	1515	95	below_threshold
Aeromonas enteropelogenes	strain=FDAARGOS_1509	GCA_020097315.1	29489	29489	type	True	87.4221	1215	1515	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	77.1747	155	1515	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.9078	153	1515	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.5695	142	1515	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.502	158	1515	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.4121	147	1515	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:09,360] [INFO] DFAST Taxonomy check result was written to GCF_020341535.1_ASM2034153v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:09,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:09,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:09,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg505e2ed2-445d-4c79-a122-be3d9756b7d4/dqc_reference/checkm_data
[2024-01-24 11:35:09,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:09,408] [INFO] Task started: CheckM
[2024-01-24 11:35:09,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020341535.1_ASM2034153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020341535.1_ASM2034153v1_genomic.fna/checkm_input GCF_020341535.1_ASM2034153v1_genomic.fna/checkm_result
[2024-01-24 11:35:52,353] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:52,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:52,375] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:52,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:52,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020341535.1_ASM2034153v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:52,376] [INFO] Task started: Blastn
[2024-01-24 11:35:52,376] [INFO] Running command: blastn -query GCF_020341535.1_ASM2034153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg505e2ed2-445d-4c79-a122-be3d9756b7d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_020341535.1_ASM2034153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:53,884] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:53,887] [INFO] Selected 11 target genomes.
[2024-01-24 11:35:53,888] [INFO] Target genome list was writen to GCF_020341535.1_ASM2034153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:53,894] [INFO] Task started: fastANI
[2024-01-24 11:35:53,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg47a3e228-d189-4e04-9ef7-b95c41d1c737/GCF_020341535.1_ASM2034153v1_genomic.fna.gz --refList GCF_020341535.1_ASM2034153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020341535.1_ASM2034153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:05,590] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:05,601] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:05,602] [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_000819955.1	s__Aeromonas jandaei	99.946	1467	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	conclusive
GCF_000764665.1	s__Aeromonas lacus	95.787	1322	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.97	96.97	0.94	0.94	2	-
GCF_019048265.1	s__Aeromonas veronii_A	90.9204	1273	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.07	95.82	0.91	0.90	4	-
GCF_000820225.1	s__Aeromonas veronii	90.7951	1256	1515	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	90.1616	1187	1515	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	89.5529	1113	1515	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	89.3604	1052	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014805.1	s__Aeromonas hydrophila	88.0748	1214	1515	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	87.6642	1213	1515	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	87.2585	1195	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	-
GCF_000820085.1	s__Aeromonas sanarellii	86.0886	1046	1515	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:05,603] [INFO] GTDB search result was written to GCF_020341535.1_ASM2034153v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:05,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:05,608] [INFO] DFAST_QC result json was written to GCF_020341535.1_ASM2034153v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:05,608] [INFO] DFAST_QC completed!
[2024-01-24 11:36:05,608] [INFO] Total running time: 0h1m26s