[2024-01-24 13:19:28,985] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:28,987] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:28,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg48296231-38d8-498c-bd3d-33e10db44568/dqc_reference
[2024-01-24 13:19:30,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:30,320] [INFO] Task started: Prodigal
[2024-01-24 13:19:30,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg8752ce11-efe2-4f27-baca-8b3ae503a80a/GCF_902170765.1_CIP109351_genomic.fna.gz | prodigal -d GCF_902170765.1_CIP109351_genomic.fna/cds.fna -a GCF_902170765.1_CIP109351_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:43,065] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:43,065] [INFO] Task started: HMMsearch
[2024-01-24 13:19:43,066] [INFO] Running command: hmmsearch --tblout GCF_902170765.1_CIP109351_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48296231-38d8-498c-bd3d-33e10db44568/dqc_reference/reference_markers.hmm GCF_902170765.1_CIP109351_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:43,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:43,375] [INFO] Found 6/6 markers.
[2024-01-24 13:19:43,417] [INFO] Query marker FASTA was written to GCF_902170765.1_CIP109351_genomic.fna/markers.fasta
[2024-01-24 13:19:43,418] [INFO] Task started: Blastn
[2024-01-24 13:19:43,418] [INFO] Running command: blastn -query GCF_902170765.1_CIP109351_genomic.fna/markers.fasta -db /var/lib/cwl/stg48296231-38d8-498c-bd3d-33e10db44568/dqc_reference/reference_markers.fasta -out GCF_902170765.1_CIP109351_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:44,287] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:44,291] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:44,292] [INFO] Target genome list was writen to GCF_902170765.1_CIP109351_genomic.fna/target_genomes.txt
[2024-01-24 13:19:44,305] [INFO] Task started: fastANI
[2024-01-24 13:19:44,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg8752ce11-efe2-4f27-baca-8b3ae503a80a/GCF_902170765.1_CIP109351_genomic.fna.gz --refList GCF_902170765.1_CIP109351_genomic.fna/target_genomes.txt --output GCF_902170765.1_CIP109351_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:59,007] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:59,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48296231-38d8-498c-bd3d-33e10db44568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:59,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48296231-38d8-498c-bd3d-33e10db44568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:59,024] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:59,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:59,024] [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 massiliensis		GCA_902170765.1	419257	419257	suspected-type	True	100.0	1503	1528	95	conclusive
Yersinia massiliensis	strain=CCUG 53443	GCA_000312485.1	419257	419257	suspected-type	True	99.9835	1490	1528	95	conclusive
Yersinia aleksiciae	strain=159	GCA_001047675.1	263819	263819	type	True	86.1126	1023	1528	95	below_threshold
Yersinia bercovieri	strain=ATCC 43970	GCA_000167975.1	634	634	type	True	85.6193	1040	1528	95	below_threshold
Yersinia bercovieri	strain=ATCC 43970	GCA_013282745.1	634	634	type	True	85.611	1085	1528	95	below_threshold
Yersinia mollaretii	strain=ATCC 43969	GCA_013282725.1	33060	33060	type	True	85.5688	1139	1528	95	below_threshold
Yersinia mollaretii	strain=ATCC 43969	GCA_000167995.1	33060	33060	type	True	85.537	1096	1528	95	below_threshold
Yersinia artesiana	strain=IP42281	GCA_902726545.1	2890315	2890315	type	True	83.5376	948	1528	95	below_threshold
Yersinia rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	83.3966	973	1528	95	below_threshold
Yersinia proxima	strain=IP37424	GCA_902170785.1	2890316	2890316	type	True	83.3334	1033	1528	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	82.8862	884	1528	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.0756	329	1528	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.9979	360	1528	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.7918	380	1528	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.6461	357	1528	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:59,026] [INFO] DFAST Taxonomy check result was written to GCF_902170765.1_CIP109351_genomic.fna/tc_result.tsv
[2024-01-24 13:19:59,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:59,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:59,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48296231-38d8-498c-bd3d-33e10db44568/dqc_reference/checkm_data
[2024-01-24 13:19:59,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:59,083] [INFO] Task started: CheckM
[2024-01-24 13:19:59,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902170765.1_CIP109351_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902170765.1_CIP109351_genomic.fna/checkm_input GCF_902170765.1_CIP109351_genomic.fna/checkm_result
[2024-01-24 13:20:39,464] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:39,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:39,490] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:39,490] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:39,491] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902170765.1_CIP109351_genomic.fna/markers.fasta)
[2024-01-24 13:20:39,491] [INFO] Task started: Blastn
[2024-01-24 13:20:39,491] [INFO] Running command: blastn -query GCF_902170765.1_CIP109351_genomic.fna/markers.fasta -db /var/lib/cwl/stg48296231-38d8-498c-bd3d-33e10db44568/dqc_reference/reference_markers_gtdb.fasta -out GCF_902170765.1_CIP109351_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:40,471] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:40,475] [INFO] Selected 14 target genomes.
[2024-01-24 13:20:40,475] [INFO] Target genome list was writen to GCF_902170765.1_CIP109351_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:40,493] [INFO] Task started: fastANI
[2024-01-24 13:20:40,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg8752ce11-efe2-4f27-baca-8b3ae503a80a/GCF_902170765.1_CIP109351_genomic.fna.gz --refList GCF_902170765.1_CIP109351_genomic.fna/target_genomes_gtdb.txt --output GCF_902170765.1_CIP109351_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:54,338] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:54,353] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:54,354] [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_000312485.1	s__Yersinia massiliensis	99.9835	1490	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.58	95.54	0.91	0.88	22	conclusive
GCF_001047675.1	s__Yersinia aleksiciae	86.1239	1022	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_013282745.1	s__Yersinia bercovieri	85.6262	1083	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.12	95.38	0.94	0.87	18	-
GCF_013282725.1	s__Yersinia mollaretii	85.5688	1139	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.95	95.82	0.92	0.88	25	-
GCF_001098625.1	s__Yersinia frederiksenii_C	83.7454	1052	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_009831415.1	s__Yersinia canariae	83.6427	1012	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
GCF_900635455.1	s__Yersinia intermedia	83.5807	1012	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.02	97.82	0.92	0.88	29	-
GCF_001152565.1	s__Yersinia pekkanenii	83.5541	933	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_001123825.1	s__Yersinia kristensenii_C	83.5337	934	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_902726525.1	s__Yersinia enterocolitica_H	83.488	977	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_003600645.1	s__Yersinia rochesterensis	83.4014	972	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_001995075.1	s__Yersinia enterocolitica_F	83.2835	1037	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_900460525.1	s__Yersinia kristensenii	83.2187	1000	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_000821185.2	s__Serratia symbiotica	78.3524	257	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.16	96.03	0.89	0.83	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:54,355] [INFO] GTDB search result was written to GCF_902170765.1_CIP109351_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:54,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:54,359] [INFO] DFAST_QC result json was written to GCF_902170765.1_CIP109351_genomic.fna/dqc_result.json
[2024-01-24 13:20:54,359] [INFO] DFAST_QC completed!
[2024-01-24 13:20:54,359] [INFO] Total running time: 0h1m25s