[2024-01-24 13:57:00,886] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,892] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg14a7ad56-939e-4ca0-8a4b-dc6de11cb3c5/dqc_reference
[2024-01-24 13:57:02,165] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,166] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,166] [INFO] Running command: gunzip -c /var/lib/cwl/stg23f340ae-7c7b-4e4c-81de-7cccd3f449b1/GCF_003600645.1_ASM360064v1_genomic.fna.gz | prodigal -d GCF_003600645.1_ASM360064v1_genomic.fna/cds.fna -a GCF_003600645.1_ASM360064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:16,712] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:16,712] [INFO] Task started: HMMsearch
[2024-01-24 13:57:16,712] [INFO] Running command: hmmsearch --tblout GCF_003600645.1_ASM360064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14a7ad56-939e-4ca0-8a4b-dc6de11cb3c5/dqc_reference/reference_markers.hmm GCF_003600645.1_ASM360064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:17,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:17,076] [INFO] Found 6/6 markers.
[2024-01-24 13:57:17,120] [INFO] Query marker FASTA was written to GCF_003600645.1_ASM360064v1_genomic.fna/markers.fasta
[2024-01-24 13:57:17,120] [INFO] Task started: Blastn
[2024-01-24 13:57:17,120] [INFO] Running command: blastn -query GCF_003600645.1_ASM360064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14a7ad56-939e-4ca0-8a4b-dc6de11cb3c5/dqc_reference/reference_markers.fasta -out GCF_003600645.1_ASM360064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:17,943] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:17,946] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:17,947] [INFO] Target genome list was writen to GCF_003600645.1_ASM360064v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:17,953] [INFO] Task started: fastANI
[2024-01-24 13:57:17,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg23f340ae-7c7b-4e4c-81de-7cccd3f449b1/GCF_003600645.1_ASM360064v1_genomic.fna.gz --refList GCF_003600645.1_ASM360064v1_genomic.fna/target_genomes.txt --output GCF_003600645.1_ASM360064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:36,097] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:36,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14a7ad56-939e-4ca0-8a4b-dc6de11cb3c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:36,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14a7ad56-939e-4ca0-8a4b-dc6de11cb3c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:36,116] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:36,117] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:57:36,117] [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 rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	100.0	1479	1482	95	inconclusive
Yersinia thracica	strain=IP34646	GCA_902170565.1	2890319	2890319	type	True	95.0119	1216	1482	95	inconclusive
Yersinia kristensenii	strain=NCTC11471	GCA_900460525.1	28152	28152	type	True	93.0058	1295	1482	95	below_threshold
Yersinia kristensenii	strain=ATCC 33638	GCA_000173715.1	28152	28152	type	True	92.8602	1267	1482	95	below_threshold
Yersinia enterocolitica	strain=ATCC 9610	GCA_000755055.1	630	630	type	True	88.1912	1184	1482	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NCTC12982	GCA_901472495.1	150052	630	type	True	88.1481	1189	1482	95	below_threshold
Yersinia enterocolitica subsp. palearctica	strain=Y11	GCA_000253175.1	150053	630	type	True	88.1356	1188	1482	95	below_threshold
Yersinia artesiana	strain=IP42281	GCA_902726545.1	2890315	2890315	type	True	88.0955	1126	1482	95	below_threshold
Yersinia proxima	strain=IP37424	GCA_902170785.1	2890316	2890316	type	True	87.8546	1196	1482	95	below_threshold
Yersinia canariae	strain=NCTC 14382	GCA_009831415.1	2607663	2607663	type	True	87.6888	1245	1482	95	below_threshold
Yersinia hibernica	strain=CFS1934	GCA_004124235.1	2339259	2339259	type	True	86.8091	1201	1482	95	below_threshold
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	85.4578	1184	1482	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	84.6174	982	1482	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.5878	413	1482	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.0416	399	1482	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.0008	384	1482	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.7573	389	1482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:36,118] [INFO] DFAST Taxonomy check result was written to GCF_003600645.1_ASM360064v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:36,119] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:36,119] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:36,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14a7ad56-939e-4ca0-8a4b-dc6de11cb3c5/dqc_reference/checkm_data
[2024-01-24 13:57:36,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:36,162] [INFO] Task started: CheckM
[2024-01-24 13:57:36,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003600645.1_ASM360064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003600645.1_ASM360064v1_genomic.fna/checkm_input GCF_003600645.1_ASM360064v1_genomic.fna/checkm_result
[2024-01-24 13:58:23,158] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:23,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:23,178] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:23,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:23,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003600645.1_ASM360064v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:23,179] [INFO] Task started: Blastn
[2024-01-24 13:58:23,179] [INFO] Running command: blastn -query GCF_003600645.1_ASM360064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14a7ad56-939e-4ca0-8a4b-dc6de11cb3c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003600645.1_ASM360064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,488] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,493] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:24,493] [INFO] Target genome list was writen to GCF_003600645.1_ASM360064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:24,502] [INFO] Task started: fastANI
[2024-01-24 13:58:24,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg23f340ae-7c7b-4e4c-81de-7cccd3f449b1/GCF_003600645.1_ASM360064v1_genomic.fna.gz --refList GCF_003600645.1_ASM360064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003600645.1_ASM360064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:36,779] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:36,794] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:36,794] [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_003600645.1	s__Yersinia rochesterensis	100.0	1479	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	conclusive
GCF_001123825.1	s__Yersinia kristensenii_C	94.9648	1256	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_900460525.1	s__Yersinia kristensenii	93.0058	1295	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_901472495.1	s__Yersinia enterocolitica	88.1447	1189	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_902726525.1	s__Yersinia enterocolitica_H	87.9479	1181	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_001995075.1	s__Yersinia enterocolitica_F	87.7588	1207	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_009831415.1	s__Yersinia canariae	87.6623	1248	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
GCF_004124235.1	s__Yersinia hibernica	86.8275	1201	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_001098625.1	s__Yersinia frederiksenii_C	85.44	1171	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_001047675.1	s__Yersinia aleksiciae	85.1057	1001	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,796] [INFO] GTDB search result was written to GCF_003600645.1_ASM360064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:36,796] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:36,800] [INFO] DFAST_QC result json was written to GCF_003600645.1_ASM360064v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:36,800] [INFO] DFAST_QC completed!
[2024-01-24 13:58:36,800] [INFO] Total running time: 0h1m36s