[2024-01-24 10:57:21,099] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:21,101] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:21,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg8da04146-5fec-4d30-93e3-49e5c8add177/dqc_reference
[2024-01-24 10:57:22,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:22,323] [INFO] Task started: Prodigal
[2024-01-24 10:57:22,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bf4594e-6ba9-4a2c-b9bd-58dc66ebd9c7/GCF_003367375.1_ASM336737v1_genomic.fna.gz | prodigal -d GCF_003367375.1_ASM336737v1_genomic.fna/cds.fna -a GCF_003367375.1_ASM336737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:34,206] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:34,206] [INFO] Task started: HMMsearch
[2024-01-24 10:57:34,206] [INFO] Running command: hmmsearch --tblout GCF_003367375.1_ASM336737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8da04146-5fec-4d30-93e3-49e5c8add177/dqc_reference/reference_markers.hmm GCF_003367375.1_ASM336737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:34,499] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:34,500] [INFO] Found 6/6 markers.
[2024-01-24 10:57:34,535] [INFO] Query marker FASTA was written to GCF_003367375.1_ASM336737v1_genomic.fna/markers.fasta
[2024-01-24 10:57:34,535] [INFO] Task started: Blastn
[2024-01-24 10:57:34,535] [INFO] Running command: blastn -query GCF_003367375.1_ASM336737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8da04146-5fec-4d30-93e3-49e5c8add177/dqc_reference/reference_markers.fasta -out GCF_003367375.1_ASM336737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:35,326] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:35,330] [INFO] Selected 22 target genomes.
[2024-01-24 10:57:35,330] [INFO] Target genome list was writen to GCF_003367375.1_ASM336737v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:35,357] [INFO] Task started: fastANI
[2024-01-24 10:57:35,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf4594e-6ba9-4a2c-b9bd-58dc66ebd9c7/GCF_003367375.1_ASM336737v1_genomic.fna.gz --refList GCF_003367375.1_ASM336737v1_genomic.fna/target_genomes.txt --output GCF_003367375.1_ASM336737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:52,902] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:52,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8da04146-5fec-4d30-93e3-49e5c8add177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:52,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8da04146-5fec-4d30-93e3-49e5c8add177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:52,918] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:52,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:52,919] [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
Gallaecimonas mangrovi	strain=HK-28	GCA_003367375.1	2291597	2291597	type	True	100.0	1357	1357	95	conclusive
Gallaecimonas pentaromativorans	strain=DSM 21945	GCA_003751625.1	584787	584787	type	True	80.477	724	1357	95	below_threshold
Gallaecimonas xiamenensis	strain=3-C-1	GCA_000299915.1	1207039	1207039	type	True	79.6948	495	1357	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.4737	62	1357	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	78.1688	73	1357	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_1523	GCA_020341535.1	650	650	type	True	78.1083	79	1357	95	below_threshold
Aeromonas jandaei	strain=FDAARGOS_986	GCA_016127195.1	650	650	type	True	78.0591	79	1357	95	below_threshold
Shewanella khirikhana	strain=TH2012	GCA_003957745.1	1965282	1965282	type	True	77.7906	111	1357	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.6988	51	1357	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	77.6517	72	1357	95	below_threshold
Aeromonas media	strain=CECT 4232	GCA_000819985.1	651	651	type	True	77.168	62	1357	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	76.8839	83	1357	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	76.8298	61	1357	95	below_threshold
Ferrimonas aestuarii	strain=IMCC35002	GCA_005116665.1	2569539	2569539	type	True	76.5637	55	1357	95	below_threshold
Aeromonas jandaei	strain=CECT 4228	GCA_000819955.1	650	650	type	True	76.4536	68	1357	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.3702	92	1357	95	below_threshold
Ferrimonas senticii	strain=DSM 18821	GCA_000422665.1	394566	394566	type	True	76.1241	74	1357	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	75.7888	75	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:52,921] [INFO] DFAST Taxonomy check result was written to GCF_003367375.1_ASM336737v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:52,921] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:52,921] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:52,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8da04146-5fec-4d30-93e3-49e5c8add177/dqc_reference/checkm_data
[2024-01-24 10:57:52,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:52,964] [INFO] Task started: CheckM
[2024-01-24 10:57:52,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367375.1_ASM336737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367375.1_ASM336737v1_genomic.fna/checkm_input GCF_003367375.1_ASM336737v1_genomic.fna/checkm_result
[2024-01-24 10:58:30,435] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:30,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:30,452] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:30,452] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:30,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367375.1_ASM336737v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:30,453] [INFO] Task started: Blastn
[2024-01-24 10:58:30,453] [INFO] Running command: blastn -query GCF_003367375.1_ASM336737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8da04146-5fec-4d30-93e3-49e5c8add177/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367375.1_ASM336737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:31,773] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:31,776] [INFO] Selected 19 target genomes.
[2024-01-24 10:58:31,776] [INFO] Target genome list was writen to GCF_003367375.1_ASM336737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:31,806] [INFO] Task started: fastANI
[2024-01-24 10:58:31,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf4594e-6ba9-4a2c-b9bd-58dc66ebd9c7/GCF_003367375.1_ASM336737v1_genomic.fna.gz --refList GCF_003367375.1_ASM336737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367375.1_ASM336737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:45,265] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:45,277] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:45,278] [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_003367375.1	s__Gallaecimonas mangrovi	100.0	1357	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Gallaecimonadaceae;g__Gallaecimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003751625.1	s__Gallaecimonas pentaromativorans	80.4649	726	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Gallaecimonadaceae;g__Gallaecimonas	95.0	98.58	98.58	0.94	0.94	2	-
GCF_000299915.1	s__Gallaecimonas xiamenensis	79.7058	495	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Gallaecimonadaceae;g__Gallaecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001521715.1	s__Enterobacter asburiae	78.3109	74	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_003957745.1	s__Shewanella khirikhana	77.7615	112	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765445.1	s__Erwinia sp009765445	77.3748	58	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819985.1	s__Aeromonas media	77.1695	63	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_010974825.1	s__Aeromonas rivipollensis	77.0711	63	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.26	95.18	0.91	0.86	15	-
GCF_002936955.1	s__Oceanisphaera arctica	76.7949	68	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001022965.1	s__Enterobacter cloacae_L	76.5761	56	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.51	97.16	0.91	0.90	5	-
GCF_005116665.1	s__Ferrimonas sp005116665	76.5272	54	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819955.1	s__Aeromonas jandaei	76.4849	67	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
GCF_018596335.1	s__Shewanella sp018596335	76.3151	92	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422665.1	s__Ferrimonas senticii	76.1241	74	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422645.1	s__Ferrimonas futtsuensis	75.7703	76	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:45,280] [INFO] GTDB search result was written to GCF_003367375.1_ASM336737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:45,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:45,284] [INFO] DFAST_QC result json was written to GCF_003367375.1_ASM336737v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:45,285] [INFO] DFAST_QC completed!
[2024-01-24 10:58:45,285] [INFO] Total running time: 0h1m24s