[2024-01-24 10:57:13,223] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,229] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,229] [INFO] DQC Reference Directory: /var/lib/cwl/stg5447e3a3-9679-4019-9c4c-a0b4edd34a37/dqc_reference
[2024-01-24 10:57:14,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,696] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,696] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbe325c7-1d7b-4a4e-9c4c-d61fc5a0a512/GCF_900636035.1_38656_G01_genomic.fna.gz | prodigal -d GCF_900636035.1_38656_G01_genomic.fna/cds.fna -a GCF_900636035.1_38656_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:26,093] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:26,094] [INFO] Task started: HMMsearch
[2024-01-24 10:57:26,094] [INFO] Running command: hmmsearch --tblout GCF_900636035.1_38656_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5447e3a3-9679-4019-9c4c-a0b4edd34a37/dqc_reference/reference_markers.hmm GCF_900636035.1_38656_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:26,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:26,423] [INFO] Found 6/6 markers.
[2024-01-24 10:57:26,468] [INFO] Query marker FASTA was written to GCF_900636035.1_38656_G01_genomic.fna/markers.fasta
[2024-01-24 10:57:26,468] [INFO] Task started: Blastn
[2024-01-24 10:57:26,468] [INFO] Running command: blastn -query GCF_900636035.1_38656_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg5447e3a3-9679-4019-9c4c-a0b4edd34a37/dqc_reference/reference_markers.fasta -out GCF_900636035.1_38656_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:27,297] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:27,300] [INFO] Selected 18 target genomes.
[2024-01-24 10:57:27,301] [INFO] Target genome list was writen to GCF_900636035.1_38656_G01_genomic.fna/target_genomes.txt
[2024-01-24 10:57:27,312] [INFO] Task started: fastANI
[2024-01-24 10:57:27,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe325c7-1d7b-4a4e-9c4c-d61fc5a0a512/GCF_900636035.1_38656_G01_genomic.fna.gz --refList GCF_900636035.1_38656_G01_genomic.fna/target_genomes.txt --output GCF_900636035.1_38656_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:46,272] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:46,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5447e3a3-9679-4019-9c4c-a0b4edd34a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:46,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5447e3a3-9679-4019-9c4c-a0b4edd34a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:46,288] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:57:46,288] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:46,288] [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
Shimwellia blattae	strain=NCTC12127	GCA_900636035.1	563	563	type	True	100.0	1384	1384	95	conclusive
Shimwellia blattae	strain=DSM 4481	GCA_000262305.1	563	563	type	True	99.9907	1381	1384	95	conclusive
Shimwellia blattae	strain=NBRC 105725	GCA_000327265.1	563	563	type	True	99.9603	1307	1384	95	conclusive
Shimwellia pseudoproteus	strain=DSM 3038	GCA_016415625.1	570012	570012	type	True	84.6231	983	1384	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	80.1984	615	1384	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	80.0543	604	1384	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	79.8738	630	1384	95	below_threshold
Atlantibacter hermannii	strain=FDAARGOS_888	GCA_016027855.1	565	565	type	True	79.8303	552	1384	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_000409225.1	413498	413497	type	True	79.7869	615	1384	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	79.7864	549	1384	95	below_threshold
Cedecea davisae	strain=DSM 4568	GCA_000412335.2	158484	158484	type	True	79.7825	585	1384	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	79.7355	569	1384	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	79.6912	555	1384	95	below_threshold
Raoultella terrigena	strain=NBRC 14941	GCA_006539725.1	577	577	type	True	79.6806	644	1384	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	79.6758	579	1384	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	79.5777	594	1384	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	79.5378	621	1384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:46,290] [INFO] DFAST Taxonomy check result was written to GCF_900636035.1_38656_G01_genomic.fna/tc_result.tsv
[2024-01-24 10:57:46,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:46,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:46,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5447e3a3-9679-4019-9c4c-a0b4edd34a37/dqc_reference/checkm_data
[2024-01-24 10:57:46,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:46,334] [INFO] Task started: CheckM
[2024-01-24 10:57:46,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900636035.1_38656_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900636035.1_38656_G01_genomic.fna/checkm_input GCF_900636035.1_38656_G01_genomic.fna/checkm_result
[2024-01-24 10:58:23,995] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:23,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:24,012] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:24,013] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:24,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900636035.1_38656_G01_genomic.fna/markers.fasta)
[2024-01-24 10:58:24,014] [INFO] Task started: Blastn
[2024-01-24 10:58:24,014] [INFO] Running command: blastn -query GCF_900636035.1_38656_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg5447e3a3-9679-4019-9c4c-a0b4edd34a37/dqc_reference/reference_markers_gtdb.fasta -out GCF_900636035.1_38656_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:25,248] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:25,252] [INFO] Selected 24 target genomes.
[2024-01-24 10:58:25,252] [INFO] Target genome list was writen to GCF_900636035.1_38656_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:25,273] [INFO] Task started: fastANI
[2024-01-24 10:58:25,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe325c7-1d7b-4a4e-9c4c-d61fc5a0a512/GCF_900636035.1_38656_G01_genomic.fna.gz --refList GCF_900636035.1_38656_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900636035.1_38656_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:47,913] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:47,939] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:47,939] [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_000262305.1	s__Shimwellia blattae	99.9907	1381	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Shimwellia	95.0	99.99	99.99	1.00	1.00	4	conclusive
GCF_016415625.1	s__Shimwellia pseudoproteus	84.6231	983	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Shimwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000982825.1	s__Cronobacter sakazakii	80.1952	618	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
GCF_000828055.2	s__Klebsiella variicola	80.1163	671	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	80.1154	671	1384	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_900021175.1	s__Enterobacter_A timonensis	80.1122	624	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001277215.2	s__Cronobacter malonaticus	80.1047	621	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_001277235.1	s__Cronobacter dublinensis	79.9886	630	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCA_900635495.1	s__Atlantibacter hermannii	79.9376	532	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.95	98.59	0.96	0.90	28	-
GCF_000742135.1	s__Klebsiella pneumoniae	79.8911	664	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_000757825.1	s__Cedecea neteri_A	79.8832	576	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	99.14	99.14	0.92	0.92	2	-
GCF_000759815.1	s__Citrobacter_A rodentium	79.8226	574	1384	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_009363175.1	s__Citrobacter_A telavivensis	79.8177	568	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001484765.1	s__Erwinia_A teleogrylli	79.7885	646	1384	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_000412335.2	s__Cedecea davisae	79.7793	586	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	98.19	96.20	0.94	0.89	6	-
GCF_009907385.1	s__Atlantibacter hermannii_A	79.7746	607	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193285.1	s__Atlantibacter sp002345315	79.6941	635	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.54	98.53	0.93	0.90	4	-
GCF_000696575.1	s__Siccibacter colletis	79.688	590	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539725.1	s__Klebsiella terrigena	79.6806	644	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.25	96.63	0.88	0.85	68	-
GCF_011752815.1	s__Cedecea sp011752815	79.6135	546	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353845.1	s__Citrobacter freundii_E	79.4954	557	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_010231475.1	s__Citrobacter sp010231475	79.3406	506	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011077955.1	s__Atlantibacter sp002358165	79.3303	516	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	99.01	98.64	0.96	0.94	5	-
GCF_900079995.3	s__Citrobacter europaeus	79.1426	545	1384	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:47,941] [INFO] GTDB search result was written to GCF_900636035.1_38656_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:47,941] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:47,945] [INFO] DFAST_QC result json was written to GCF_900636035.1_38656_G01_genomic.fna/dqc_result.json
[2024-01-24 10:58:47,945] [INFO] DFAST_QC completed!
[2024-01-24 10:58:47,946] [INFO] Total running time: 0h1m35s