[2024-01-25 19:00:35,664] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:35,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:35,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg187c582c-932e-4de0-9ed9-fb7c0b2df171/dqc_reference
[2024-01-25 19:00:36,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:36,786] [INFO] Task started: Prodigal
[2024-01-25 19:00:36,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg5666b199-4219-4877-b08a-e63a6d7bf22c/GCF_025215155.1_ASM2521515v1_genomic.fna.gz | prodigal -d GCF_025215155.1_ASM2521515v1_genomic.fna/cds.fna -a GCF_025215155.1_ASM2521515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:49,093] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:49,093] [INFO] Task started: HMMsearch
[2024-01-25 19:00:49,093] [INFO] Running command: hmmsearch --tblout GCF_025215155.1_ASM2521515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg187c582c-932e-4de0-9ed9-fb7c0b2df171/dqc_reference/reference_markers.hmm GCF_025215155.1_ASM2521515v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:49,393] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:49,394] [INFO] Found 6/6 markers.
[2024-01-25 19:00:49,436] [INFO] Query marker FASTA was written to GCF_025215155.1_ASM2521515v1_genomic.fna/markers.fasta
[2024-01-25 19:00:49,436] [INFO] Task started: Blastn
[2024-01-25 19:00:49,436] [INFO] Running command: blastn -query GCF_025215155.1_ASM2521515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg187c582c-932e-4de0-9ed9-fb7c0b2df171/dqc_reference/reference_markers.fasta -out GCF_025215155.1_ASM2521515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:50,251] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:50,255] [INFO] Selected 26 target genomes.
[2024-01-25 19:00:50,256] [INFO] Target genome list was writen to GCF_025215155.1_ASM2521515v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:50,271] [INFO] Task started: fastANI
[2024-01-25 19:00:50,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg5666b199-4219-4877-b08a-e63a6d7bf22c/GCF_025215155.1_ASM2521515v1_genomic.fna.gz --refList GCF_025215155.1_ASM2521515v1_genomic.fna/target_genomes.txt --output GCF_025215155.1_ASM2521515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:15,983] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:15,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg187c582c-932e-4de0-9ed9-fb7c0b2df171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:15,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg187c582c-932e-4de0-9ed9-fb7c0b2df171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:15,997] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:01:15,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:01:15,998] [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	82.3972	823	1704	95	below_threshold
Buttiauxella izardii	strain=CCUG 35510	GCA_003601925.1	82991	82991	type	True	82.1104	936	1704	95	below_threshold
Buttiauxella agrestis	strain=ATCC 33320	GCA_000735355.1	82977	82977	type	True	81.9225	868	1704	95	below_threshold
Buttiauxella agrestis	strain=NCTC12119	GCA_900446255.1	82977	82977	type	True	81.9107	935	1704	95	below_threshold
Cedecea davisae	strain=NCTC13724	GCA_900446735.1	158484	158484	type	True	81.8646	877	1704	95	below_threshold
Cedecea davisae	strain=DSM 4568	GCA_000412335.2	158484	158484	type	True	81.7818	887	1704	95	below_threshold
Cedecea lapagei	strain=NCTC11466	GCA_900635955.1	158823	158823	type	True	81.7806	849	1704	95	below_threshold
Buttiauxella gaviniae	strain=ATCC 51604	GCA_001654835.1	82990	82990	type	True	81.7619	865	1704	95	below_threshold
Buttiauxella ferragutiae	strain=ATCC 51602	GCA_001654915.1	82989	82989	type	True	81.7613	858	1704	95	below_threshold
Buttiauxella brennerae	strain=ATCC 51605	GCA_001654925.1	82988	82988	type	True	81.7371	922	1704	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	81.6779	853	1704	95	below_threshold
Cedecea neteri	strain=NBRC 105707	GCA_001571265.1	158822	158822	suspected-type	True	81.6036	859	1704	95	below_threshold
Buttiauxella noackiae	strain=ATCC 51607	GCA_001654865.1	82992	82992	type	True	81.6029	865	1704	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.7865	784	1704	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.4579	755	1704	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	80.4078	778	1704	95	below_threshold
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	80.4041	735	1704	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	80.2725	671	1704	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	80.2626	743	1704	95	below_threshold
Cronobacter dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	80.2482	746	1704	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_000409225.1	413498	413497	type	True	80.1623	738	1704	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_009646115.1	470933	470933	type	True	78.3719	433	1704	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_006494355.1	470933	470933	type	True	78.3677	428	1704	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	78.3388	379	1704	95	below_threshold
Leminorella richardii	strain=NCTC12151	GCA_900478135.1	158841	158841	type	True	77.5112	209	1704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:15,999] [INFO] DFAST Taxonomy check result was written to GCF_025215155.1_ASM2521515v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:15,999] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:16,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:16,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg187c582c-932e-4de0-9ed9-fb7c0b2df171/dqc_reference/checkm_data
[2024-01-25 19:01:16,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:16,050] [INFO] Task started: CheckM
[2024-01-25 19:01:16,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025215155.1_ASM2521515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025215155.1_ASM2521515v1_genomic.fna/checkm_input GCF_025215155.1_ASM2521515v1_genomic.fna/checkm_result
[2024-01-25 19:01:55,398] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:55,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:55,422] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:55,423] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:55,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025215155.1_ASM2521515v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:55,423] [INFO] Task started: Blastn
[2024-01-25 19:01:55,423] [INFO] Running command: blastn -query GCF_025215155.1_ASM2521515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg187c582c-932e-4de0-9ed9-fb7c0b2df171/dqc_reference/reference_markers_gtdb.fasta -out GCF_025215155.1_ASM2521515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:56,624] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:56,631] [INFO] Selected 19 target genomes.
[2024-01-25 19:01:56,632] [INFO] Target genome list was writen to GCF_025215155.1_ASM2521515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:56,647] [INFO] Task started: fastANI
[2024-01-25 19:01:56,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg5666b199-4219-4877-b08a-e63a6d7bf22c/GCF_025215155.1_ASM2521515v1_genomic.fna.gz --refList GCF_025215155.1_ASM2521515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025215155.1_ASM2521515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:18,144] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:18,164] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:18,164] [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	96.9397	1476	1704	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	84.0789	1002	1704	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	83.9074	994	1704	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	82.423	821	1704	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	82.1059	935	1704	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	81.9403	864	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	96.92	96.37	0.91	0.90	3	-
GCF_000412335.2	s__Cedecea davisae	81.7791	886	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	98.19	96.20	0.94	0.89	6	-
GCF_900635955.1	s__Cedecea lapagei	81.758	852	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654925.1	s__Buttiauxella brennerae	81.7152	925	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902500225.1	s__Buttiauxella agrestis_A	81.6995	850	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	95.69	95.69	0.85	0.85	2	-
GCF_011752815.1	s__Cedecea sp011752815	81.6347	835	1704	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	81.6262	862	1704	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	81.4454	860	1704	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	81.3888	827	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018323985.1	s__Enterobacter_D kobei_A	80.3648	734	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	99.37	98.44	0.98	0.93	6	-
GCF_013927005.1	s__Enterobacter sp013927005	80.1935	708	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735365.1	s__Kluyvera ascorbata	80.0981	683	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.94	97.70	0.94	0.89	5	-
GCF_009914055.1	s__Mixta intestinalis	78.5133	453	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517625.1	s__Mixta tenebrionis	78.4952	480	1704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.45	99.45	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:18,166] [INFO] GTDB search result was written to GCF_025215155.1_ASM2521515v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:18,166] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:18,170] [INFO] DFAST_QC result json was written to GCF_025215155.1_ASM2521515v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:18,170] [INFO] DFAST_QC completed!
[2024-01-25 19:02:18,170] [INFO] Total running time: 0h1m43s