[2024-01-25 19:10:05,469] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:05,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:05,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cdaea0f-94c0-47a9-827d-ecb83f7093ed/dqc_reference
[2024-01-25 19:10:06,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:06,562] [INFO] Task started: Prodigal
[2024-01-25 19:10:06,562] [INFO] Running command: gunzip -c /var/lib/cwl/stg02584436-28b5-4b17-a2da-a0b2efeb9ea2/GCF_000412335.2_ASM41233v2_genomic.fna.gz | prodigal -d GCF_000412335.2_ASM41233v2_genomic.fna/cds.fna -a GCF_000412335.2_ASM41233v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:18,361] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:18,361] [INFO] Task started: HMMsearch
[2024-01-25 19:10:18,361] [INFO] Running command: hmmsearch --tblout GCF_000412335.2_ASM41233v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cdaea0f-94c0-47a9-827d-ecb83f7093ed/dqc_reference/reference_markers.hmm GCF_000412335.2_ASM41233v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:18,670] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:18,671] [INFO] Found 6/6 markers.
[2024-01-25 19:10:18,711] [INFO] Query marker FASTA was written to GCF_000412335.2_ASM41233v2_genomic.fna/markers.fasta
[2024-01-25 19:10:18,712] [INFO] Task started: Blastn
[2024-01-25 19:10:18,712] [INFO] Running command: blastn -query GCF_000412335.2_ASM41233v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cdaea0f-94c0-47a9-827d-ecb83f7093ed/dqc_reference/reference_markers.fasta -out GCF_000412335.2_ASM41233v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:19,593] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:19,595] [INFO] Selected 15 target genomes.
[2024-01-25 19:10:19,596] [INFO] Target genome list was writen to GCF_000412335.2_ASM41233v2_genomic.fna/target_genomes.txt
[2024-01-25 19:10:19,609] [INFO] Task started: fastANI
[2024-01-25 19:10:19,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg02584436-28b5-4b17-a2da-a0b2efeb9ea2/GCF_000412335.2_ASM41233v2_genomic.fna.gz --refList GCF_000412335.2_ASM41233v2_genomic.fna/target_genomes.txt --output GCF_000412335.2_ASM41233v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:36,121] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:36,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cdaea0f-94c0-47a9-827d-ecb83f7093ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:36,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cdaea0f-94c0-47a9-827d-ecb83f7093ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:36,131] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:10:36,132] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:36,132] [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
Cedecea davisae	strain=DSM 4568	GCA_000412335.2	158484	158484	type	True	99.9998	1627	1628	95	conclusive
Cedecea davisae	strain=NCTC13724	GCA_900446735.1	158484	158484	type	True	99.9731	1613	1628	95	conclusive
Cedecea neteri	strain=NBRC 105707	GCA_001571265.1	158822	158822	suspected-type	True	86.0995	1214	1628	95	below_threshold
Cedecea lapagei	strain=NCTC11466	GCA_900635955.1	158823	158823	type	True	85.8971	1213	1628	95	below_threshold
Buttiauxella warmboldiae	strain=CCUG 35512	GCA_003818135.1	82993	82993	type	True	81.5077	751	1628	95	below_threshold
Buttiauxella agrestis	strain=NCTC12119	GCA_900446255.1	82977	82977	type	True	80.9994	822	1628	95	below_threshold
Buttiauxella brennerae	strain=ATCC 51605	GCA_001654925.1	82988	82988	type	True	80.8126	787	1628	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	80.7921	758	1628	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.7388	804	1628	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	80.6822	786	1628	95	below_threshold
Kluyvera sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	80.4847	744	1628	95	below_threshold
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	80.4381	731	1628	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	80.4011	756	1628	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	80.3496	699	1628	95	below_threshold
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	80.3374	748	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:36,142] [INFO] DFAST Taxonomy check result was written to GCF_000412335.2_ASM41233v2_genomic.fna/tc_result.tsv
[2024-01-25 19:10:36,143] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:36,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:36,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cdaea0f-94c0-47a9-827d-ecb83f7093ed/dqc_reference/checkm_data
[2024-01-25 19:10:36,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:36,206] [INFO] Task started: CheckM
[2024-01-25 19:10:36,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000412335.2_ASM41233v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000412335.2_ASM41233v2_genomic.fna/checkm_input GCF_000412335.2_ASM41233v2_genomic.fna/checkm_result
[2024-01-25 19:11:12,875] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:12,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:12,892] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:12,893] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:12,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000412335.2_ASM41233v2_genomic.fna/markers.fasta)
[2024-01-25 19:11:12,893] [INFO] Task started: Blastn
[2024-01-25 19:11:12,893] [INFO] Running command: blastn -query GCF_000412335.2_ASM41233v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cdaea0f-94c0-47a9-827d-ecb83f7093ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_000412335.2_ASM41233v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:14,326] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:14,331] [INFO] Selected 10 target genomes.
[2024-01-25 19:11:14,331] [INFO] Target genome list was writen to GCF_000412335.2_ASM41233v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:14,341] [INFO] Task started: fastANI
[2024-01-25 19:11:14,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg02584436-28b5-4b17-a2da-a0b2efeb9ea2/GCF_000412335.2_ASM41233v2_genomic.fna.gz --refList GCF_000412335.2_ASM41233v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000412335.2_ASM41233v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:26,590] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:26,597] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:26,597] [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_000412335.2	s__Cedecea davisae	99.9998	1627	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	98.19	96.20	0.94	0.89	6	conclusive
GCF_000757825.1	s__Cedecea neteri_A	86.5448	1305	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	99.14	99.14	0.92	0.92	2	-
GCA_009668225.1	s__Cedecea sp009668225	86.2702	1259	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571265.1	s__Cedecea neteri	86.1099	1213	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	99.91	99.83	0.99	0.99	3	-
GCF_900635955.1	s__Cedecea lapagei	85.908	1212	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963575.1	s__Cedecea michiganensis_A	85.7809	1270	1628	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	85.741	1233	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000277545.1	s__Cedecea sp000277545	85.7166	1234	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	98.25	97.46	0.94	0.91	5	-
GCF_011752815.1	s__Cedecea sp011752815	85.6199	1239	1628	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	85.5603	1276	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	97.60	97.60	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:26,599] [INFO] GTDB search result was written to GCF_000412335.2_ASM41233v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:26,599] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:26,602] [INFO] DFAST_QC result json was written to GCF_000412335.2_ASM41233v2_genomic.fna/dqc_result.json
[2024-01-25 19:11:26,602] [INFO] DFAST_QC completed!
[2024-01-25 19:11:26,602] [INFO] Total running time: 0h1m21s