[2024-01-24 14:22:04,572] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,574] [INFO] DQC Reference Directory: /var/lib/cwl/stg31c557d3-1c70-40a1-b9a6-ae03ccb016b5/dqc_reference
[2024-01-24 14:22:05,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,926] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,926] [INFO] Running command: gunzip -c /var/lib/cwl/stgbad8eb57-f324-4cb7-a8a6-3caf3532ef45/GCF_900457155.1_57940_C01_genomic.fna.gz | prodigal -d GCF_900457155.1_57940_C01_genomic.fna/cds.fna -a GCF_900457155.1_57940_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:20,307] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:20,307] [INFO] Task started: HMMsearch
[2024-01-24 14:22:20,308] [INFO] Running command: hmmsearch --tblout GCF_900457155.1_57940_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31c557d3-1c70-40a1-b9a6-ae03ccb016b5/dqc_reference/reference_markers.hmm GCF_900457155.1_57940_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:20,617] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:20,618] [INFO] Found 6/6 markers.
[2024-01-24 14:22:20,662] [INFO] Query marker FASTA was written to GCF_900457155.1_57940_C01_genomic.fna/markers.fasta
[2024-01-24 14:22:20,663] [INFO] Task started: Blastn
[2024-01-24 14:22:20,663] [INFO] Running command: blastn -query GCF_900457155.1_57940_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg31c557d3-1c70-40a1-b9a6-ae03ccb016b5/dqc_reference/reference_markers.fasta -out GCF_900457155.1_57940_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:21,560] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:21,578] [INFO] Selected 12 target genomes.
[2024-01-24 14:22:21,579] [INFO] Target genome list was writen to GCF_900457155.1_57940_C01_genomic.fna/target_genomes.txt
[2024-01-24 14:22:21,581] [INFO] Task started: fastANI
[2024-01-24 14:22:21,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad8eb57-f324-4cb7-a8a6-3caf3532ef45/GCF_900457155.1_57940_C01_genomic.fna.gz --refList GCF_900457155.1_57940_C01_genomic.fna/target_genomes.txt --output GCF_900457155.1_57940_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:22,312] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:22,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31c557d3-1c70-40a1-b9a6-ae03ccb016b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:22,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31c557d3-1c70-40a1-b9a6-ae03ccb016b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:22,326] [WARNING] Following organisms are indistinguishable with ANI. [Escherichia coli(562), Shigella boydii(621), Shigella dysenteriae(622), Shigella flexneri(623), Shigella sonnei(624)]
[2024-01-24 14:23:22,327] [INFO] Found 12 fastANI hits (9 hits with ANI > threshold)
[2024-01-24 14:23:22,327] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2024-01-24 14:23:22,327] [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 sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	100.0	1688	1691	95	indistinguishable
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	99.9971	1662	1691	95	indistinguishable
Shigella boydii	strain=DMB SH130	GCA_003572535.1	621	621	type	True	98.325	1034	1691	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	98.0409	1319	1691	95	indistinguishable
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	97.9684	1317	1691	95	indistinguishable
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	97.8803	1339	1691	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	96.5729	1297	1691	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	96.4659	1270	1691	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	96.4593	1320	1691	95	indistinguishable
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	90.2182	1174	1691	95	below_threshold
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	90.1245	1108	1691	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	82.268	830	1691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:22,329] [INFO] DFAST Taxonomy check result was written to GCF_900457155.1_57940_C01_genomic.fna/tc_result.tsv
[2024-01-24 14:23:22,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:22,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:22,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31c557d3-1c70-40a1-b9a6-ae03ccb016b5/dqc_reference/checkm_data
[2024-01-24 14:23:22,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:22,387] [INFO] Task started: CheckM
[2024-01-24 14:23:22,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900457155.1_57940_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900457155.1_57940_C01_genomic.fna/checkm_input GCF_900457155.1_57940_C01_genomic.fna/checkm_result
[2024-01-24 14:24:05,474] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:05,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:05,499] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:05,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:05,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900457155.1_57940_C01_genomic.fna/markers.fasta)
[2024-01-24 14:24:05,501] [INFO] Task started: Blastn
[2024-01-24 14:24:05,501] [INFO] Running command: blastn -query GCF_900457155.1_57940_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg31c557d3-1c70-40a1-b9a6-ae03ccb016b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900457155.1_57940_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:06,667] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:06,675] [INFO] Selected 12 target genomes.
[2024-01-24 14:24:06,675] [INFO] Target genome list was writen to GCF_900457155.1_57940_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:06,680] [INFO] Task started: fastANI
[2024-01-24 14:24:06,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad8eb57-f324-4cb7-a8a6-3caf3532ef45/GCF_900457155.1_57940_C01_genomic.fna.gz --refList GCF_900457155.1_57940_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900457155.1_57940_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:22,342] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:22,357] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:22,358] [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_003697165.2	s__Escherichia coli	96.5691	1294	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	conclusive
GCF_002965065.1	s__Escherichia sp002965065	94.1859	1084	1691	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	92.7462	1247	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
GCF_004211955.1	s__Escherichia sp004211955	92.6495	1221	1691	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	92.5228	1273	1691	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	92.0954	1171	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660175.1	s__Escherichia sp001660175	91.5033	1230	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.53	99.22	0.94	0.92	3	-
GCF_000026225.1	s__Escherichia fergusonii	91.1375	1065	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
GCF_002900365.1	s__Escherichia marmotae	90.9462	1242	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	-
GCF_000759775.1	s__Escherichia albertii	90.1344	1107	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.47	97.95	0.90	0.82	107	-
GCF_000981805.1	s__Citrobacter_A amalonaticus_C	82.6315	975	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342285.1	s__Klebsiella sp004342285	80.7345	738	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:22,359] [INFO] GTDB search result was written to GCF_900457155.1_57940_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:22,360] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:22,363] [INFO] DFAST_QC result json was written to GCF_900457155.1_57940_C01_genomic.fna/dqc_result.json
[2024-01-24 14:24:22,363] [INFO] DFAST_QC completed!
[2024-01-24 14:24:22,364] [INFO] Total running time: 0h2m18s