[2024-01-25 19:03:20,683] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:20,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:20,685] [INFO] DQC Reference Directory: /var/lib/cwl/stgc064d70e-a363-437d-9b85-02e1de11c40e/dqc_reference
[2024-01-25 19:03:21,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:21,857] [INFO] Task started: Prodigal
[2024-01-25 19:03:21,857] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6b83c68-21fc-4012-8e6d-402026042b9d/GCF_000764665.1_ASM76466v1_genomic.fna.gz | prodigal -d GCF_000764665.1_ASM76466v1_genomic.fna/cds.fna -a GCF_000764665.1_ASM76466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:33,275] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:33,276] [INFO] Task started: HMMsearch
[2024-01-25 19:03:33,276] [INFO] Running command: hmmsearch --tblout GCF_000764665.1_ASM76466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc064d70e-a363-437d-9b85-02e1de11c40e/dqc_reference/reference_markers.hmm GCF_000764665.1_ASM76466v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:33,567] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:33,568] [INFO] Found 6/6 markers.
[2024-01-25 19:03:33,604] [INFO] Query marker FASTA was written to GCF_000764665.1_ASM76466v1_genomic.fna/markers.fasta
[2024-01-25 19:03:33,605] [INFO] Task started: Blastn
[2024-01-25 19:03:33,605] [INFO] Running command: blastn -query GCF_000764665.1_ASM76466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc064d70e-a363-437d-9b85-02e1de11c40e/dqc_reference/reference_markers.fasta -out GCF_000764665.1_ASM76466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:34,507] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:34,510] [INFO] Selected 16 target genomes.
[2024-01-25 19:03:34,511] [INFO] Target genome list was writen to GCF_000764665.1_ASM76466v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:34,521] [INFO] Task started: fastANI
[2024-01-25 19:03:34,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6b83c68-21fc-4012-8e6d-402026042b9d/GCF_000764665.1_ASM76466v1_genomic.fna.gz --refList GCF_000764665.1_ASM76466v1_genomic.fna/target_genomes.txt --output GCF_000764665.1_ASM76466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:49,723] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:49,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc064d70e-a363-437d-9b85-02e1de11c40e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:49,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc064d70e-a363-437d-9b85-02e1de11c40e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:49,734] [INFO] Found 16 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:03:49,735] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:03:49,735] [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 lacus	strain=AE122	GCA_000764665.1	558884	558884	type	True	100.0	1374	1380	95	inconclusive
Aeromonas jandaei	strain=CECT 4228	GCA_000819955.1	650	650	type	True	95.8323	1286	1380	95	inconclusive
Aeromonas jandaei	strain=FDAARGOS_986	GCA_016127195.1	650	650	type	True	95.8144	1328	1380	95	inconclusive
Aeromonas jandaei	strain=FDAARGOS_1523	GCA_020341535.1	650	650	type	True	95.7997	1329	1380	95	inconclusive
Aeromonas veronii	strain=ATCC 35624	GCA_018359905.1	654	654	type	True	90.9358	1195	1380	95	below_threshold
Aeromonas veronii	strain=CECT 4257	GCA_000820225.1	654	654	type	True	90.9122	1181	1380	95	below_threshold
Aeromonas finlandensis	strain=4287D	GCA_000764645.1	1543375	1543375	type	True	90.5553	1128	1380	95	below_threshold
Aeromonas australiensis	strain=CECT 8023	GCA_000819725.1	1114880	1114880	type	True	89.6293	1067	1380	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	87.8608	1137	1380	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	87.7804	1155	1380	95	below_threshold
Aeromonas enteropelogenes	strain=FDAARGOS_1509	GCA_020097315.1	29489	29489	type	True	87.3431	1149	1380	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.7648	132	1380	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.3456	113	1380	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	76.2672	115	1380	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.2612	116	1380	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	76.0748	102	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:49,736] [INFO] DFAST Taxonomy check result was written to GCF_000764665.1_ASM76466v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:49,737] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:49,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:49,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc064d70e-a363-437d-9b85-02e1de11c40e/dqc_reference/checkm_data
[2024-01-25 19:03:49,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:49,786] [INFO] Task started: CheckM
[2024-01-25 19:03:49,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000764665.1_ASM76466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000764665.1_ASM76466v1_genomic.fna/checkm_input GCF_000764665.1_ASM76466v1_genomic.fna/checkm_result
[2024-01-25 19:04:24,800] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:24,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:24,820] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:24,821] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:24,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000764665.1_ASM76466v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:24,822] [INFO] Task started: Blastn
[2024-01-25 19:04:24,822] [INFO] Running command: blastn -query GCF_000764665.1_ASM76466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc064d70e-a363-437d-9b85-02e1de11c40e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000764665.1_ASM76466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:26,296] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:26,299] [INFO] Selected 12 target genomes.
[2024-01-25 19:04:26,299] [INFO] Target genome list was writen to GCF_000764665.1_ASM76466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:26,308] [INFO] Task started: fastANI
[2024-01-25 19:04:26,308] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6b83c68-21fc-4012-8e6d-402026042b9d/GCF_000764665.1_ASM76466v1_genomic.fna.gz --refList GCF_000764665.1_ASM76466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000764665.1_ASM76466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:38,647] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:38,661] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:38,662] [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_000764665.1	s__Aeromonas lacus	100.0	1374	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.97	96.97	0.94	0.94	2	conclusive
GCF_000819955.1	s__Aeromonas jandaei	95.8323	1286	1380	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_000820225.1	s__Aeromonas veronii	90.9122	1181	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.01	0.90	0.86	159	-
GCF_019048265.1	s__Aeromonas veronii_A	90.7763	1211	1380	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	90.5512	1129	1380	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	89.6293	1067	1380	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	89.466	1025	1380	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	88.9608	1062	1380	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	87.9282	1165	1380	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	87.7689	1156	1380	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	87.386	1128	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	-
GCF_000819785.1	s__Aeromonas caviae	86.1252	1015	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:38,664] [INFO] GTDB search result was written to GCF_000764665.1_ASM76466v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:38,664] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:38,668] [INFO] DFAST_QC result json was written to GCF_000764665.1_ASM76466v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:38,668] [INFO] DFAST_QC completed!
[2024-01-25 19:04:38,668] [INFO] Total running time: 0h1m18s