[2024-01-24 14:30:44,768] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:44,770] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:44,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c410d6b-0c5b-44ea-8d41-d16636e4f462/dqc_reference
[2024-01-24 14:30:46,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:46,084] [INFO] Task started: Prodigal
[2024-01-24 14:30:46,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg3aece621-2c87-4d85-8371-2b68af746a9e/GCF_004124235.1_ASM412423v1_genomic.fna.gz | prodigal -d GCF_004124235.1_ASM412423v1_genomic.fna/cds.fna -a GCF_004124235.1_ASM412423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:59,106] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:59,106] [INFO] Task started: HMMsearch
[2024-01-24 14:30:59,106] [INFO] Running command: hmmsearch --tblout GCF_004124235.1_ASM412423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c410d6b-0c5b-44ea-8d41-d16636e4f462/dqc_reference/reference_markers.hmm GCF_004124235.1_ASM412423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:59,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:59,434] [INFO] Found 6/6 markers.
[2024-01-24 14:30:59,487] [INFO] Query marker FASTA was written to GCF_004124235.1_ASM412423v1_genomic.fna/markers.fasta
[2024-01-24 14:30:59,487] [INFO] Task started: Blastn
[2024-01-24 14:30:59,488] [INFO] Running command: blastn -query GCF_004124235.1_ASM412423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c410d6b-0c5b-44ea-8d41-d16636e4f462/dqc_reference/reference_markers.fasta -out GCF_004124235.1_ASM412423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:00,300] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:00,306] [INFO] Selected 23 target genomes.
[2024-01-24 14:31:00,307] [INFO] Target genome list was writen to GCF_004124235.1_ASM412423v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:00,319] [INFO] Task started: fastANI
[2024-01-24 14:31:00,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aece621-2c87-4d85-8371-2b68af746a9e/GCF_004124235.1_ASM412423v1_genomic.fna.gz --refList GCF_004124235.1_ASM412423v1_genomic.fna/target_genomes.txt --output GCF_004124235.1_ASM412423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:22,994] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:22,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c410d6b-0c5b-44ea-8d41-d16636e4f462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:22,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c410d6b-0c5b-44ea-8d41-d16636e4f462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:23,021] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:23,022] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:23,022] [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
Yersinia hibernica	strain=CFS1934	GCA_004124235.1	2339259	2339259	type	True	100.0	1594	1600	95	conclusive
Yersinia canariae	strain=NCTC 14382	GCA_009831415.1	2607663	2607663	type	True	90.1167	1323	1600	95	below_threshold
Yersinia thracica	strain=IP34646	GCA_902170565.1	2890319	2890319	type	True	86.8564	1158	1600	95	below_threshold
Yersinia rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	86.7717	1208	1600	95	below_threshold
Yersinia artesiana	strain=IP42281	GCA_902726545.1	2890315	2890315	type	True	86.5854	1152	1600	95	below_threshold
Yersinia kristensenii	strain=NCTC11471	GCA_900460525.1	28152	28152	type	True	86.5779	1234	1600	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NCTC12982	GCA_901472495.1	150052	630	type	True	86.4747	1216	1600	95	below_threshold
Yersinia kristensenii	strain=ATCC 33638	GCA_000173715.1	28152	28152	type	True	86.4636	1198	1600	95	below_threshold
Yersinia enterocolitica subsp. palearctica	strain=NCTC13769	GCA_900637005.1	150053	630	type	True	86.4029	1215	1600	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NBRC 105693	GCA_001598735.1	150052	630	type	True	86.4018	1178	1600	95	below_threshold
Yersinia enterocolitica subsp. palearctica	strain=Y11	GCA_000253175.1	150053	630	type	True	86.395	1204	1600	95	below_threshold
Yersinia enterocolitica	strain=ATCC 9610	GCA_000755055.1	630	630	type	True	86.38	1218	1600	95	below_threshold
Yersinia proxima	strain=IP37424	GCA_902170785.1	2890316	2890316	type	True	86.2873	1220	1600	95	below_threshold
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	85.97	1187	1600	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	83.8309	1019	1600	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.3929	414	1600	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.3106	353	1600	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.6806	337	1600	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	77.9987	253	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:23,024] [INFO] DFAST Taxonomy check result was written to GCF_004124235.1_ASM412423v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:23,024] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:23,024] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:23,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c410d6b-0c5b-44ea-8d41-d16636e4f462/dqc_reference/checkm_data
[2024-01-24 14:31:23,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:23,076] [INFO] Task started: CheckM
[2024-01-24 14:31:23,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004124235.1_ASM412423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004124235.1_ASM412423v1_genomic.fna/checkm_input GCF_004124235.1_ASM412423v1_genomic.fna/checkm_result
[2024-01-24 14:32:05,848] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:05,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:05,875] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:05,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:05,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004124235.1_ASM412423v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:05,877] [INFO] Task started: Blastn
[2024-01-24 14:32:05,877] [INFO] Running command: blastn -query GCF_004124235.1_ASM412423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c410d6b-0c5b-44ea-8d41-d16636e4f462/dqc_reference/reference_markers_gtdb.fasta -out GCF_004124235.1_ASM412423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:06,916] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:06,920] [INFO] Selected 15 target genomes.
[2024-01-24 14:32:06,920] [INFO] Target genome list was writen to GCF_004124235.1_ASM412423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:06,933] [INFO] Task started: fastANI
[2024-01-24 14:32:06,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aece621-2c87-4d85-8371-2b68af746a9e/GCF_004124235.1_ASM412423v1_genomic.fna.gz --refList GCF_004124235.1_ASM412423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004124235.1_ASM412423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:22,296] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:22,313] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:22,313] [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_004124235.1	s__Yersinia hibernica	100.0	1595	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	conclusive
GCF_009831415.1	s__Yersinia canariae	90.1167	1323	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
GCF_001123825.1	s__Yersinia kristensenii_C	86.7846	1173	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_003600645.1	s__Yersinia rochesterensis	86.762	1207	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_900460525.1	s__Yersinia kristensenii	86.5779	1234	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_902726525.1	s__Yersinia enterocolitica_H	86.489	1207	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_901472495.1	s__Yersinia enterocolitica	86.4711	1216	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_001995075.1	s__Yersinia enterocolitica_F	86.3213	1236	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_001098625.1	s__Yersinia frederiksenii_C	85.9227	1217	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_000754805.1	s__Yersinia frederiksenii	85.5492	1226	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	-
GCF_900635455.1	s__Yersinia intermedia	84.135	1117	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.02	97.82	0.92	0.88	29	-
GCF_002847015.1	s__ATCC-39006 sp002847015	78.92	270	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__ATCC-39006	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014639435.1	s__Ewingella psychrotolerans	78.6562	337	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:22,315] [INFO] GTDB search result was written to GCF_004124235.1_ASM412423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:22,315] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:22,319] [INFO] DFAST_QC result json was written to GCF_004124235.1_ASM412423v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:22,320] [INFO] DFAST_QC completed!
[2024-01-24 14:32:22,320] [INFO] Total running time: 0h1m38s