[2024-01-25 18:49:20,610] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:20,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:20,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d362a14-78cf-4b42-bd2c-d2afdd8f452f/dqc_reference
[2024-01-25 18:49:21,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:21,793] [INFO] Task started: Prodigal
[2024-01-25 18:49:21,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d69a759-ccb3-4229-9204-5d9d4eebda60/GCF_014836715.1_ASM1483671v1_genomic.fna.gz | prodigal -d GCF_014836715.1_ASM1483671v1_genomic.fna/cds.fna -a GCF_014836715.1_ASM1483671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:32,473] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:32,473] [INFO] Task started: HMMsearch
[2024-01-25 18:49:32,473] [INFO] Running command: hmmsearch --tblout GCF_014836715.1_ASM1483671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d362a14-78cf-4b42-bd2c-d2afdd8f452f/dqc_reference/reference_markers.hmm GCF_014836715.1_ASM1483671v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:32,703] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:32,706] [INFO] Found 6/6 markers.
[2024-01-25 18:49:32,745] [INFO] Query marker FASTA was written to GCF_014836715.1_ASM1483671v1_genomic.fna/markers.fasta
[2024-01-25 18:49:32,745] [INFO] Task started: Blastn
[2024-01-25 18:49:32,745] [INFO] Running command: blastn -query GCF_014836715.1_ASM1483671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d362a14-78cf-4b42-bd2c-d2afdd8f452f/dqc_reference/reference_markers.fasta -out GCF_014836715.1_ASM1483671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:33,553] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:33,555] [INFO] Selected 17 target genomes.
[2024-01-25 18:49:33,556] [INFO] Target genome list was writen to GCF_014836715.1_ASM1483671v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:33,580] [INFO] Task started: fastANI
[2024-01-25 18:49:33,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d69a759-ccb3-4229-9204-5d9d4eebda60/GCF_014836715.1_ASM1483671v1_genomic.fna.gz --refList GCF_014836715.1_ASM1483671v1_genomic.fna/target_genomes.txt --output GCF_014836715.1_ASM1483671v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:54,080] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:54,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d362a14-78cf-4b42-bd2c-d2afdd8f452f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:54,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d362a14-78cf-4b42-bd2c-d2afdd8f452f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:54,092] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:49:54,092] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:49:54,092] [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
Shigella boydii	strain=DMB SH130	GCA_003572535.1	621	621	type	True	91.9011	957	1500	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	91.8754	1301	1500	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	91.82	1282	1500	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	91.7832	1251	1500	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	91.7638	1291	1500	95	below_threshold
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	91.6091	1219	1500	95	below_threshold
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	91.5869	1204	1500	95	below_threshold
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	91.5113	1146	1500	95	below_threshold
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	91.5043	1137	1500	95	below_threshold
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	91.498	1197	1500	95	below_threshold
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	91.2794	1140	1500	95	below_threshold
Shigella dysenteriae	strain=NCTC4837	GCA_900457215.1	622	622	suspected-type	True	91.1876	1152	1500	95	below_threshold
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	89.765	1096	1500	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	89.5878	1167	1500	95	below_threshold
Escherichia fergusonii	strain=FDAARGOS_1499	GCA_020097475.1	564	564	type	True	89.2169	1101	1500	95	below_threshold
Escherichia fergusonii	strain=ATCC 35469T	GCA_000026225.1	564	564	type	True	89.2063	1098	1500	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.9571	821	1500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:54,094] [INFO] DFAST Taxonomy check result was written to GCF_014836715.1_ASM1483671v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:54,094] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:54,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:54,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d362a14-78cf-4b42-bd2c-d2afdd8f452f/dqc_reference/checkm_data
[2024-01-25 18:49:54,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:54,139] [INFO] Task started: CheckM
[2024-01-25 18:49:54,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836715.1_ASM1483671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836715.1_ASM1483671v1_genomic.fna/checkm_input GCF_014836715.1_ASM1483671v1_genomic.fna/checkm_result
[2024-01-25 18:50:27,741] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:27,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:27,759] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:27,760] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:27,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836715.1_ASM1483671v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:27,760] [INFO] Task started: Blastn
[2024-01-25 18:50:27,761] [INFO] Running command: blastn -query GCF_014836715.1_ASM1483671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d362a14-78cf-4b42-bd2c-d2afdd8f452f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836715.1_ASM1483671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:28,873] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:28,875] [INFO] Selected 8 target genomes.
[2024-01-25 18:50:28,875] [INFO] Target genome list was writen to GCF_014836715.1_ASM1483671v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:28,883] [INFO] Task started: fastANI
[2024-01-25 18:50:28,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d69a759-ccb3-4229-9204-5d9d4eebda60/GCF_014836715.1_ASM1483671v1_genomic.fna.gz --refList GCF_014836715.1_ASM1483671v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836715.1_ASM1483671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:38,044] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:38,051] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:38,051] [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_001660175.1	s__Escherichia sp001660175	99.1907	1447	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.53	99.22	0.94	0.92	3	conclusive
GCF_004211955.1	s__Escherichia sp004211955	94.8214	1316	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005843885.1	s__Escherichia sp005843885	94.7449	1352	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_011881725.1	s__Escherichia coli_E	92.9042	1203	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498915.1	s__Escherichia ruysiae	92.0218	1283	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
GCF_003697165.2	s__Escherichia coli	91.82	1282	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	-
GCF_002900365.1	s__Escherichia marmotae	91.154	1293	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	-
GCF_000026225.1	s__Escherichia fergusonii	89.2067	1098	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:38,053] [INFO] GTDB search result was written to GCF_014836715.1_ASM1483671v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:38,055] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:38,057] [INFO] DFAST_QC result json was written to GCF_014836715.1_ASM1483671v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:38,058] [INFO] DFAST_QC completed!
[2024-01-25 18:50:38,058] [INFO] Total running time: 0h1m17s