[2024-01-24 11:27:04,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg9da4d257-4b07-43c7-852e-a4d2ecadc214/dqc_reference
[2024-01-24 11:27:05,729] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,729] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,730] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f994223-8597-40ea-bfa3-c66d6df5a75f/GCF_016756775.1_ASM1675677v1_genomic.fna.gz | prodigal -d GCF_016756775.1_ASM1675677v1_genomic.fna/cds.fna -a GCF_016756775.1_ASM1675677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:18,916] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:18,917] [INFO] Task started: HMMsearch
[2024-01-24 11:27:18,917] [INFO] Running command: hmmsearch --tblout GCF_016756775.1_ASM1675677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9da4d257-4b07-43c7-852e-a4d2ecadc214/dqc_reference/reference_markers.hmm GCF_016756775.1_ASM1675677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:19,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:19,222] [INFO] Found 6/6 markers.
[2024-01-24 11:27:19,266] [INFO] Query marker FASTA was written to GCF_016756775.1_ASM1675677v1_genomic.fna/markers.fasta
[2024-01-24 11:27:19,266] [INFO] Task started: Blastn
[2024-01-24 11:27:19,266] [INFO] Running command: blastn -query GCF_016756775.1_ASM1675677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9da4d257-4b07-43c7-852e-a4d2ecadc214/dqc_reference/reference_markers.fasta -out GCF_016756775.1_ASM1675677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:20,177] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:20,179] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:20,180] [INFO] Target genome list was writen to GCF_016756775.1_ASM1675677v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:20,212] [INFO] Task started: fastANI
[2024-01-24 11:27:20,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f994223-8597-40ea-bfa3-c66d6df5a75f/GCF_016756775.1_ASM1675677v1_genomic.fna.gz --refList GCF_016756775.1_ASM1675677v1_genomic.fna/target_genomes.txt --output GCF_016756775.1_ASM1675677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:37,886] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:37,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9da4d257-4b07-43c7-852e-a4d2ecadc214/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:37,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9da4d257-4b07-43c7-852e-a4d2ecadc214/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:37,911] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:37,911] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:37,911] [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
Buttiauxella warmboldiae	strain=CCUG 35512	GCA_003818135.1	82993	82993	type	True	82.2731	835	1674	95	below_threshold
Buttiauxella izardii	strain=CCUG 35510	GCA_003601925.1	82991	82991	type	True	81.9882	941	1674	95	below_threshold
Cedecea davisae	strain=DSM 4568	GCA_000412335.2	158484	158484	type	True	81.8758	882	1674	95	below_threshold
Cedecea davisae	strain=NCTC13724	GCA_900446735.1	158484	158484	type	True	81.8367	882	1674	95	below_threshold
Buttiauxella agrestis	strain=NCTC12119	GCA_900446255.1	82977	82977	type	True	81.7371	937	1674	95	below_threshold
Buttiauxella agrestis	strain=ATCC 33320	GCA_000735355.1	82977	82977	type	True	81.6982	911	1674	95	below_threshold
Buttiauxella brennerae	strain=ATCC 51605	GCA_001654925.1	82988	82988	type	True	81.6919	906	1674	95	below_threshold
Buttiauxella gaviniae	strain=ATCC 51604	GCA_001654835.1	82990	82990	type	True	81.6584	870	1674	95	below_threshold
Cedecea neteri	strain=NBRC 105707	GCA_001571265.1	158822	158822	suspected-type	True	81.6555	860	1674	95	below_threshold
Cedecea lapagei	strain=NCTC11466	GCA_900635955.1	158823	158823	type	True	81.645	866	1674	95	below_threshold
Buttiauxella ferragutiae	strain=ATCC 51602	GCA_001654915.1	82989	82989	type	True	81.6284	860	1674	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	81.5336	860	1674	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.5548	758	1674	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	80.4512	769	1674	95	below_threshold
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	80.4082	751	1674	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	80.1647	679	1674	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	80.1097	688	1674	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	79.9264	723	1674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:37,913] [INFO] DFAST Taxonomy check result was written to GCF_016756775.1_ASM1675677v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:37,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:37,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:37,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9da4d257-4b07-43c7-852e-a4d2ecadc214/dqc_reference/checkm_data
[2024-01-24 11:27:37,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:37,965] [INFO] Task started: CheckM
[2024-01-24 11:27:37,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016756775.1_ASM1675677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016756775.1_ASM1675677v1_genomic.fna/checkm_input GCF_016756775.1_ASM1675677v1_genomic.fna/checkm_result
[2024-01-24 11:28:19,887] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:19,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:19,913] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:19,914] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:19,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016756775.1_ASM1675677v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:19,914] [INFO] Task started: Blastn
[2024-01-24 11:28:19,915] [INFO] Running command: blastn -query GCF_016756775.1_ASM1675677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9da4d257-4b07-43c7-852e-a4d2ecadc214/dqc_reference/reference_markers_gtdb.fasta -out GCF_016756775.1_ASM1675677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:21,359] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:21,363] [INFO] Selected 13 target genomes.
[2024-01-24 11:28:21,363] [INFO] Target genome list was writen to GCF_016756775.1_ASM1675677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:21,377] [INFO] Task started: fastANI
[2024-01-24 11:28:21,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f994223-8597-40ea-bfa3-c66d6df5a75f/GCF_016756775.1_ASM1675677v1_genomic.fna.gz --refList GCF_016756775.1_ASM1675677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016756775.1_ASM1675677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:35,484] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:35,507] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:35,508] [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_016756775.1	s__Buttiauxella davisae_A	100.0	1672	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003628475.1	s__Buttiauxella sp002321695	84.1869	988	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	99.11	99.11	0.94	0.94	2	-
GCF_011808225.1	s__Buttiauxella colo	83.9025	994	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003818135.1	s__Buttiauxella warmboldiae	82.2617	837	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003601925.1	s__Buttiauxella izardii	81.9735	944	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735355.1	s__Buttiauxella agrestis	81.6998	911	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	96.92	96.37	0.91	0.90	3	-
GCF_001654925.1	s__Buttiauxella brennerae	81.6919	907	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635955.1	s__Cedecea lapagei	81.6383	869	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758325.1	s__Cedecea neteri_B	81.6154	876	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752815.1	s__Cedecea sp011752815	81.5945	868	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758305.1	s__Cedecea neteri_C	81.4618	881	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	97.60	97.60	0.88	0.88	2	-
GCF_000963575.1	s__Cedecea michiganensis_A	81.3786	877	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006376615.1	s__Buttiauxella sp006376615	81.2646	832	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:35,509] [INFO] GTDB search result was written to GCF_016756775.1_ASM1675677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:35,510] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:35,516] [INFO] DFAST_QC result json was written to GCF_016756775.1_ASM1675677v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:35,516] [INFO] DFAST_QC completed!
[2024-01-24 11:28:35,516] [INFO] Total running time: 0h1m31s