[2024-01-24 15:03:14,667] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:14,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:14,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg959ea0af-b185-4884-819c-a842396b248c/dqc_reference
[2024-01-24 15:03:15,970] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:15,970] [INFO] Task started: Prodigal
[2024-01-24 15:03:15,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg4711c6dc-2298-407d-993d-d19c40009005/GCF_005671395.1_ASM567139v1_genomic.fna.gz | prodigal -d GCF_005671395.1_ASM567139v1_genomic.fna/cds.fna -a GCF_005671395.1_ASM567139v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:29,652] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:29,653] [INFO] Task started: HMMsearch
[2024-01-24 15:03:29,653] [INFO] Running command: hmmsearch --tblout GCF_005671395.1_ASM567139v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg959ea0af-b185-4884-819c-a842396b248c/dqc_reference/reference_markers.hmm GCF_005671395.1_ASM567139v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:30,021] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:30,023] [INFO] Found 6/6 markers.
[2024-01-24 15:03:30,070] [INFO] Query marker FASTA was written to GCF_005671395.1_ASM567139v1_genomic.fna/markers.fasta
[2024-01-24 15:03:30,070] [INFO] Task started: Blastn
[2024-01-24 15:03:30,071] [INFO] Running command: blastn -query GCF_005671395.1_ASM567139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg959ea0af-b185-4884-819c-a842396b248c/dqc_reference/reference_markers.fasta -out GCF_005671395.1_ASM567139v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:30,973] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:30,976] [INFO] Selected 28 target genomes.
[2024-01-24 15:03:30,977] [INFO] Target genome list was writen to GCF_005671395.1_ASM567139v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:30,993] [INFO] Task started: fastANI
[2024-01-24 15:03:30,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg4711c6dc-2298-407d-993d-d19c40009005/GCF_005671395.1_ASM567139v1_genomic.fna.gz --refList GCF_005671395.1_ASM567139v1_genomic.fna/target_genomes.txt --output GCF_005671395.1_ASM567139v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:58,362] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:58,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg959ea0af-b185-4884-819c-a842396b248c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:58,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg959ea0af-b185-4884-819c-a842396b248c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:58,382] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:58,382] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:58,383] [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
Cronobacter dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	80.147	686	1727	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	80.1391	683	1727	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	79.9338	681	1727	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_001277195.1	413501	413501	type	True	79.9257	686	1727	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_001277235.1	413498	413497	type	True	79.9128	681	1727	95	below_threshold
Siccibacter turicensis	strain=LMG 23730	GCA_000463155.2	357233	357233	type	True	79.8767	637	1727	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	79.8605	682	1727	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	79.8407	658	1727	95	below_threshold
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	79.8259	682	1727	95	below_threshold
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	79.7186	657	1727	95	below_threshold
Citrobacter rodentium	strain=NBRC 105723	GCA_000759815.1	67825	67825	type	True	79.7153	663	1727	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	79.6808	676	1727	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	79.6772	621	1727	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_000409225.1	413498	413497	type	True	79.6707	680	1727	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	79.6536	637	1727	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	79.6527	694	1727	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	79.6479	633	1727	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	79.636	672	1727	95	below_threshold
Citrobacter rodentium	strain=ATCC 51116	GCA_015965415.1	67825	67825	type	True	79.628	673	1727	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	79.5997	648	1727	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=NBRC 14940	GCA_001590945.1	72407	573	type	True	79.5314	674	1727	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	79.4723	657	1727	95	below_threshold
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	79.3491	638	1727	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	79.2735	650	1727	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	78.9583	547	1727	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:58,384] [INFO] DFAST Taxonomy check result was written to GCF_005671395.1_ASM567139v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:58,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:58,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:58,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg959ea0af-b185-4884-819c-a842396b248c/dqc_reference/checkm_data
[2024-01-24 15:03:58,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:58,436] [INFO] Task started: CheckM
[2024-01-24 15:03:58,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005671395.1_ASM567139v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005671395.1_ASM567139v1_genomic.fna/checkm_input GCF_005671395.1_ASM567139v1_genomic.fna/checkm_result
[2024-01-24 15:04:43,068] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:43,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:43,091] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:43,092] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:43,092] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005671395.1_ASM567139v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:43,093] [INFO] Task started: Blastn
[2024-01-24 15:04:43,093] [INFO] Running command: blastn -query GCF_005671395.1_ASM567139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg959ea0af-b185-4884-819c-a842396b248c/dqc_reference/reference_markers_gtdb.fasta -out GCF_005671395.1_ASM567139v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:44,252] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:44,255] [INFO] Selected 25 target genomes.
[2024-01-24 15:04:44,255] [INFO] Target genome list was writen to GCF_005671395.1_ASM567139v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:44,284] [INFO] Task started: fastANI
[2024-01-24 15:04:44,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg4711c6dc-2298-407d-993d-d19c40009005/GCF_005671395.1_ASM567139v1_genomic.fna.gz --refList GCF_005671395.1_ASM567139v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005671395.1_ASM567139v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:07,530] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:07,548] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:07,548] [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_005671395.1	s__Jejubacter calystegiae	100.0	1726	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Jejubacter	95.0	98.55	98.55	0.90	0.90	2	conclusive
GCF_001277215.2	s__Cronobacter malonaticus	80.0007	680	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCA_000027065.2	s__Cronobacter turicensis	79.9795	682	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	79.9699	675	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	98.80	98.80	0.94	0.94	2	-
GCF_000982825.1	s__Cronobacter sakazakii	79.96	673	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
GCF_001277195.1	s__Cronobacter muytjensii	79.9065	684	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCF_001277235.1	s__Cronobacter dublinensis	79.8726	680	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCF_000463155.2	s__Siccibacter turicensis	79.8723	638	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	98.74	97.87	0.95	0.92	6	-
GCA_000302695.1	s__Jejubacter sp000302695	79.8675	702	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Jejubacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002208095.1	s__Enterobacter cloacae_M	79.8184	658	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.7528	98.28	96.89	0.91	0.85	84	-
GCF_000696575.1	s__Siccibacter colletis	79.7256	654	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759815.1	s__Citrobacter_A rodentium	79.7239	663	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.98	99.96	0.98	0.96	4	-
GCF_009907385.1	s__Atlantibacter hermannii_A	79.6809	655	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002211745.1	s__Kluyvera georgiana_A	79.671	654	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
GCF_014168815.1	s__Kluyvera ascorbata_B	79.6584	646	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.36	99.08	0.90	0.88	9	-
GCA_900635495.1	s__Atlantibacter hermannii	79.6274	555	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.95	98.59	0.96	0.90	28	-
GCF_007570865.1	s__Atlantibacter subterranea	79.5978	652	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.55	98.44	0.93	0.91	8	-
GCF_009711095.1	s__Escherichia_C alba	79.4702	614	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001484765.1	s__Erwinia_A teleogrylli	79.4661	684	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000280495.2	s__Kosakonia radicincitans	79.4502	618	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
GCF_000759835.1	s__Citrobacter_A sedlakii	79.3513	583	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.16	99.00	0.95	0.93	10	-
GCF_001654985.1	s__Kluyvera georgiana	79.3481	637	1727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.06	98.06	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:07,550] [INFO] GTDB search result was written to GCF_005671395.1_ASM567139v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:07,551] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:07,556] [INFO] DFAST_QC result json was written to GCF_005671395.1_ASM567139v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:07,556] [INFO] DFAST_QC completed!
[2024-01-24 15:05:07,556] [INFO] Total running time: 0h1m53s