[2024-01-24 12:15:04,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg903be7d4-7c61-4e73-b634-543d7026a73e/dqc_reference
[2024-01-24 12:15:05,327] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,328] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,328] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f020e0c-ec15-43aa-b161-b14738f1ff96/GCF_001277255.1_ASM127725v1_genomic.fna.gz | prodigal -d GCF_001277255.1_ASM127725v1_genomic.fna/cds.fna -a GCF_001277255.1_ASM127725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:18,180] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:18,181] [INFO] Task started: HMMsearch
[2024-01-24 12:15:18,181] [INFO] Running command: hmmsearch --tblout GCF_001277255.1_ASM127725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg903be7d4-7c61-4e73-b634-543d7026a73e/dqc_reference/reference_markers.hmm GCF_001277255.1_ASM127725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:18,544] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:18,546] [INFO] Found 6/6 markers.
[2024-01-24 12:15:18,597] [INFO] Query marker FASTA was written to GCF_001277255.1_ASM127725v1_genomic.fna/markers.fasta
[2024-01-24 12:15:18,598] [INFO] Task started: Blastn
[2024-01-24 12:15:18,598] [INFO] Running command: blastn -query GCF_001277255.1_ASM127725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg903be7d4-7c61-4e73-b634-543d7026a73e/dqc_reference/reference_markers.fasta -out GCF_001277255.1_ASM127725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:19,558] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:19,562] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:19,562] [INFO] Target genome list was writen to GCF_001277255.1_ASM127725v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:19,569] [INFO] Task started: fastANI
[2024-01-24 12:15:19,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f020e0c-ec15-43aa-b161-b14738f1ff96/GCF_001277255.1_ASM127725v1_genomic.fna.gz --refList GCF_001277255.1_ASM127725v1_genomic.fna/target_genomes.txt --output GCF_001277255.1_ASM127725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:36,777] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:36,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg903be7d4-7c61-4e73-b634-543d7026a73e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:36,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg903be7d4-7c61-4e73-b634-543d7026a73e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:36,798] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:36,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:36,798] [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 condimenti	strain=LMG 26250	GCA_001277255.1	1163710	1163710	type	True	100.0	1497	1499	95	conclusive
Cronobacter condimenti	strain=1330	GCA_000319285.1	1163710	1163710	type	True	99.9128	1416	1499	95	conclusive
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_001277235.1	413498	413497	type	True	89.2369	1315	1499	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_000409225.1	413498	413497	type	True	89.1888	1284	1499	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	88.9501	1261	1499	95	below_threshold
Cronobacter dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	88.8656	1259	1499	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_001277175.1	535744	535744	type	True	88.1785	1294	1499	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_900447325.1	535744	535744	type	True	88.1444	1294	1499	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000409325.1	535744	535744	type	True	88.128	1253	1499	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_001277215.2	413503	413503	type	True	87.9541	1251	1499	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	87.8794	1232	1499	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000319325.1	535744	535744	type	True	87.8425	1271	1499	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	87.7747	1145	1499	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	80.6533	765	1499	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	80.5388	710	1499	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	80.481	754	1499	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.4428	765	1499	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:36,800] [INFO] DFAST Taxonomy check result was written to GCF_001277255.1_ASM127725v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:36,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:36,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:36,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg903be7d4-7c61-4e73-b634-543d7026a73e/dqc_reference/checkm_data
[2024-01-24 12:15:36,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:36,849] [INFO] Task started: CheckM
[2024-01-24 12:15:36,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001277255.1_ASM127725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001277255.1_ASM127725v1_genomic.fna/checkm_input GCF_001277255.1_ASM127725v1_genomic.fna/checkm_result
[2024-01-24 12:16:17,366] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:17,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:17,405] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:17,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:17,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001277255.1_ASM127725v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:17,406] [INFO] Task started: Blastn
[2024-01-24 12:16:17,406] [INFO] Running command: blastn -query GCF_001277255.1_ASM127725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg903be7d4-7c61-4e73-b634-543d7026a73e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001277255.1_ASM127725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:18,909] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:18,912] [INFO] Selected 7 target genomes.
[2024-01-24 12:16:18,913] [INFO] Target genome list was writen to GCF_001277255.1_ASM127725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:18,918] [INFO] Task started: fastANI
[2024-01-24 12:16:18,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f020e0c-ec15-43aa-b161-b14738f1ff96/GCF_001277255.1_ASM127725v1_genomic.fna.gz --refList GCF_001277255.1_ASM127725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001277255.1_ASM127725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:26,877] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:26,891] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:26,891] [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_001277255.1	s__Cronobacter condimenti	100.0	1498	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.97	99.97	0.99	0.97	3	conclusive
GCF_001277235.1	s__Cronobacter dublinensis	89.2369	1315	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCF_001277195.1	s__Cronobacter muytjensii	88.5722	1285	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCF_001277175.1	s__Cronobacter universalis	88.1908	1294	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCA_000027065.2	s__Cronobacter turicensis	88.1248	1285	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_001277215.2	s__Cronobacter malonaticus	87.9555	1251	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_000982825.1	s__Cronobacter sakazakii	87.9205	1239	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:26,895] [INFO] GTDB search result was written to GCF_001277255.1_ASM127725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:26,895] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:26,902] [INFO] DFAST_QC result json was written to GCF_001277255.1_ASM127725v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:26,902] [INFO] DFAST_QC completed!
[2024-01-24 12:16:26,902] [INFO] Total running time: 0h1m23s