[2024-01-24 13:25:30,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,680] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f977197-c0db-458f-bf09-1c33745c989c/dqc_reference
[2024-01-24 13:25:32,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,014] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,015] [INFO] Running command: gunzip -c /var/lib/cwl/stg0911776b-6fd4-4c79-be53-58131d7ccd9b/GCF_002950395.1_ASM295039v1_genomic.fna.gz | prodigal -d GCF_002950395.1_ASM295039v1_genomic.fna/cds.fna -a GCF_002950395.1_ASM295039v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:45,527] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:45,528] [INFO] Task started: HMMsearch
[2024-01-24 13:25:45,528] [INFO] Running command: hmmsearch --tblout GCF_002950395.1_ASM295039v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f977197-c0db-458f-bf09-1c33745c989c/dqc_reference/reference_markers.hmm GCF_002950395.1_ASM295039v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:45,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:45,842] [INFO] Found 6/6 markers.
[2024-01-24 13:25:45,886] [INFO] Query marker FASTA was written to GCF_002950395.1_ASM295039v1_genomic.fna/markers.fasta
[2024-01-24 13:25:45,886] [INFO] Task started: Blastn
[2024-01-24 13:25:45,886] [INFO] Running command: blastn -query GCF_002950395.1_ASM295039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f977197-c0db-458f-bf09-1c33745c989c/dqc_reference/reference_markers.fasta -out GCF_002950395.1_ASM295039v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:46,740] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:46,745] [INFO] Selected 12 target genomes.
[2024-01-24 13:25:46,746] [INFO] Target genome list was writen to GCF_002950395.1_ASM295039v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:46,754] [INFO] Task started: fastANI
[2024-01-24 13:25:46,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg0911776b-6fd4-4c79-be53-58131d7ccd9b/GCF_002950395.1_ASM295039v1_genomic.fna.gz --refList GCF_002950395.1_ASM295039v1_genomic.fna/target_genomes.txt --output GCF_002950395.1_ASM295039v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:43,947] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:43,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f977197-c0db-458f-bf09-1c33745c989c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:43,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f977197-c0db-458f-bf09-1c33745c989c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:43,963] [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 13:26:43,963] [INFO] Found 12 fastANI hits (9 hits with ANI > threshold)
[2024-01-24 13:26:43,963] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2024-01-24 13:26:43,963] [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=ATCC 29930	GCA_002950395.1	624	624	type	True	100.0	1664	1664	95	indistinguishable
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	99.9971	1661	1664	95	indistinguishable
Shigella boydii	strain=DMB SH130	GCA_003572535.1	621	621	type	True	98.3362	1034	1664	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	98.1109	1315	1664	95	indistinguishable
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	98.021	1313	1664	95	indistinguishable
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	97.869	1331	1664	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	96.5698	1299	1664	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	96.5584	1304	1664	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	96.4777	1283	1664	95	indistinguishable
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	90.294	1181	1664	95	below_threshold
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	90.1818	1099	1664	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	82.2857	845	1664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:43,965] [INFO] DFAST Taxonomy check result was written to GCF_002950395.1_ASM295039v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:43,965] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:43,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:43,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f977197-c0db-458f-bf09-1c33745c989c/dqc_reference/checkm_data
[2024-01-24 13:26:43,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:44,014] [INFO] Task started: CheckM
[2024-01-24 13:26:44,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002950395.1_ASM295039v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002950395.1_ASM295039v1_genomic.fna/checkm_input GCF_002950395.1_ASM295039v1_genomic.fna/checkm_result
[2024-01-24 13:27:26,180] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:26,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:26,204] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:26,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:26,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002950395.1_ASM295039v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:26,205] [INFO] Task started: Blastn
[2024-01-24 13:27:26,205] [INFO] Running command: blastn -query GCF_002950395.1_ASM295039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f977197-c0db-458f-bf09-1c33745c989c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002950395.1_ASM295039v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:27,318] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:27,326] [INFO] Selected 12 target genomes.
[2024-01-24 13:27:27,326] [INFO] Target genome list was writen to GCF_002950395.1_ASM295039v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:27,361] [INFO] Task started: fastANI
[2024-01-24 13:27:27,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg0911776b-6fd4-4c79-be53-58131d7ccd9b/GCF_002950395.1_ASM295039v1_genomic.fna.gz --refList GCF_002950395.1_ASM295039v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002950395.1_ASM295039v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:42,649] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:42,663] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:42,663] [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	96.5468	1306	1664	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	94.1688	1097	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004211955.1	s__Escherichia sp004211955	92.6986	1222	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902498915.1	s__Escherichia ruysiae	92.6457	1248	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
GCF_005843885.1	s__Escherichia sp005843885	92.511	1290	1664	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	92.0524	1183	1664	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	91.5446	1215	1664	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	90.9761	1057	1664	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	90.8656	1253	1664	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	90.1781	1100	1664	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	82.7352	978	1664	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	80.724	723	1664	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 13:27:42,665] [INFO] GTDB search result was written to GCF_002950395.1_ASM295039v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:42,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:42,669] [INFO] DFAST_QC result json was written to GCF_002950395.1_ASM295039v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:42,669] [INFO] DFAST_QC completed!
[2024-01-24 13:27:42,669] [INFO] Total running time: 0h2m12s