[2024-01-24 14:38:46,953] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:46,955] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:46,955] [INFO] DQC Reference Directory: /var/lib/cwl/stg075a64af-aa2a-4be1-88d2-236744f10cda/dqc_reference
[2024-01-24 14:38:48,308] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,309] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg662a580f-2d13-4aff-a638-a3d81c2022f7/GCF_002950215.1_ASM295021v1_genomic.fna.gz | prodigal -d GCF_002950215.1_ASM295021v1_genomic.fna/cds.fna -a GCF_002950215.1_ASM295021v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:01,569] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:01,570] [INFO] Task started: HMMsearch
[2024-01-24 14:39:01,570] [INFO] Running command: hmmsearch --tblout GCF_002950215.1_ASM295021v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg075a64af-aa2a-4be1-88d2-236744f10cda/dqc_reference/reference_markers.hmm GCF_002950215.1_ASM295021v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:01,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:01,855] [INFO] Found 6/6 markers.
[2024-01-24 14:39:01,899] [INFO] Query marker FASTA was written to GCF_002950215.1_ASM295021v1_genomic.fna/markers.fasta
[2024-01-24 14:39:01,900] [INFO] Task started: Blastn
[2024-01-24 14:39:01,900] [INFO] Running command: blastn -query GCF_002950215.1_ASM295021v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg075a64af-aa2a-4be1-88d2-236744f10cda/dqc_reference/reference_markers.fasta -out GCF_002950215.1_ASM295021v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:02,743] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:02,747] [INFO] Selected 14 target genomes.
[2024-01-24 14:39:02,747] [INFO] Target genome list was writen to GCF_002950215.1_ASM295021v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:02,754] [INFO] Task started: fastANI
[2024-01-24 14:39:02,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg662a580f-2d13-4aff-a638-a3d81c2022f7/GCF_002950215.1_ASM295021v1_genomic.fna.gz --refList GCF_002950215.1_ASM295021v1_genomic.fna/target_genomes.txt --output GCF_002950215.1_ASM295021v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:07,311] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:07,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg075a64af-aa2a-4be1-88d2-236744f10cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:07,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg075a64af-aa2a-4be1-88d2-236744f10cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:07,326] [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 14:40:07,326] [INFO] Found 14 fastANI hits (11 hits with ANI > threshold)
[2024-01-24 14:40:07,327] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2024-01-24 14:40:07,327] [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 flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	100.0	1639	1645	95	indistinguishable
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	97.928	1314	1645	95	indistinguishable
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	97.9076	1316	1645	95	indistinguishable
Shigella boydii	strain=DMB SH130	GCA_003572535.1	621	621	type	True	97.8254	1012	1645	95	indistinguishable
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	97.8231	1263	1645	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	97.7816	1282	1645	95	indistinguishable
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	97.0017	1240	1645	95	indistinguishable
Shigella dysenteriae	strain=NCTC4837	GCA_900457215.1	622	622	suspected-type	True	96.9516	1237	1645	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	96.4404	1247	1645	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	96.365	1232	1645	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	96.3607	1280	1645	95	indistinguishable
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	89.9058	1159	1645	95	below_threshold
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	89.7504	1078	1645	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	82.1393	824	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:07,333] [INFO] DFAST Taxonomy check result was written to GCF_002950215.1_ASM295021v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:07,334] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:07,334] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:07,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg075a64af-aa2a-4be1-88d2-236744f10cda/dqc_reference/checkm_data
[2024-01-24 14:40:07,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:07,414] [INFO] Task started: CheckM
[2024-01-24 14:40:07,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002950215.1_ASM295021v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002950215.1_ASM295021v1_genomic.fna/checkm_input GCF_002950215.1_ASM295021v1_genomic.fna/checkm_result
[2024-01-24 14:40:50,047] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:50,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:50,069] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:50,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:50,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002950215.1_ASM295021v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:50,070] [INFO] Task started: Blastn
[2024-01-24 14:40:50,070] [INFO] Running command: blastn -query GCF_002950215.1_ASM295021v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg075a64af-aa2a-4be1-88d2-236744f10cda/dqc_reference/reference_markers_gtdb.fasta -out GCF_002950215.1_ASM295021v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:51,190] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:51,193] [INFO] Selected 12 target genomes.
[2024-01-24 14:40:51,193] [INFO] Target genome list was writen to GCF_002950215.1_ASM295021v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:51,241] [INFO] Task started: fastANI
[2024-01-24 14:40:51,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg662a580f-2d13-4aff-a638-a3d81c2022f7/GCF_002950215.1_ASM295021v1_genomic.fna.gz --refList GCF_002950215.1_ASM295021v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002950215.1_ASM295021v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:05,729] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:05,740] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:05,740] [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	96.3482	1279	1645	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	94.2023	1078	1645	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	92.5914	1220	1645	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	92.557	1206	1645	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	92.2995	1243	1645	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	91.9655	1156	1645	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	91.4426	1200	1645	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	90.9912	1049	1645	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	90.827	1216	1645	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	89.8224	1071	1645	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	82.6981	942	1645	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	80.8975	710	1645	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 14:41:05,742] [INFO] GTDB search result was written to GCF_002950215.1_ASM295021v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:05,743] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:05,746] [INFO] DFAST_QC result json was written to GCF_002950215.1_ASM295021v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:05,746] [INFO] DFAST_QC completed!
[2024-01-24 14:41:05,747] [INFO] Total running time: 0h2m19s