[2024-01-25 19:59:50,393] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:50,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:50,394] [INFO] DQC Reference Directory: /var/lib/cwl/stgd248cf96-a2f0-4e63-9a8b-f2e66bbaee50/dqc_reference
[2024-01-25 19:59:51,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:51,527] [INFO] Task started: Prodigal
[2024-01-25 19:59:51,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg00c6c921-ce9e-47ce-8b9b-5b3f3cf81887/GCF_000167975.1_ASM16797v1_genomic.fna.gz | prodigal -d GCF_000167975.1_ASM16797v1_genomic.fna/cds.fna -a GCF_000167975.1_ASM16797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:00,906] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:00,906] [INFO] Task started: HMMsearch
[2024-01-25 20:00:00,906] [INFO] Running command: hmmsearch --tblout GCF_000167975.1_ASM16797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd248cf96-a2f0-4e63-9a8b-f2e66bbaee50/dqc_reference/reference_markers.hmm GCF_000167975.1_ASM16797v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:01,147] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:01,148] [INFO] Found 6/6 markers.
[2024-01-25 20:00:01,184] [INFO] Query marker FASTA was written to GCF_000167975.1_ASM16797v1_genomic.fna/markers.fasta
[2024-01-25 20:00:01,184] [INFO] Task started: Blastn
[2024-01-25 20:00:01,184] [INFO] Running command: blastn -query GCF_000167975.1_ASM16797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd248cf96-a2f0-4e63-9a8b-f2e66bbaee50/dqc_reference/reference_markers.fasta -out GCF_000167975.1_ASM16797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:01,957] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:01,960] [INFO] Selected 11 target genomes.
[2024-01-25 20:00:01,960] [INFO] Target genome list was writen to GCF_000167975.1_ASM16797v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:01,968] [INFO] Task started: fastANI
[2024-01-25 20:00:01,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c6c921-ce9e-47ce-8b9b-5b3f3cf81887/GCF_000167975.1_ASM16797v1_genomic.fna.gz --refList GCF_000167975.1_ASM16797v1_genomic.fna/target_genomes.txt --output GCF_000167975.1_ASM16797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:12,677] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:12,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd248cf96-a2f0-4e63-9a8b-f2e66bbaee50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:12,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd248cf96-a2f0-4e63-9a8b-f2e66bbaee50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:12,686] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:00:12,686] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:12,686] [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 bercovieri	strain=ATCC 43970	GCA_000167975.1	634	634	type	True	100.0	1359	1369	95	conclusive
Yersinia bercovieri	strain=ATCC 43970	GCA_013282745.1	634	634	type	True	99.9963	1367	1369	95	conclusive
Yersinia aleksiciae	strain=159	GCA_001047675.1	263819	263819	type	True	91.3085	1035	1369	95	below_threshold
Yersinia mollaretii	strain=ATCC 43969	GCA_013282725.1	33060	33060	type	True	89.8011	1147	1369	95	below_threshold
Yersinia mollaretii	strain=ATCC 43969	GCA_000167995.1	33060	33060	type	True	89.7926	1121	1369	95	below_threshold
Yersinia rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	84.5758	1028	1369	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	83.8453	939	1369	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.0917	418	1369	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.9001	415	1369	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.6531	373	1369	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.3255	171	1369	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:12,687] [INFO] DFAST Taxonomy check result was written to GCF_000167975.1_ASM16797v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:12,688] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:12,688] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:12,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd248cf96-a2f0-4e63-9a8b-f2e66bbaee50/dqc_reference/checkm_data
[2024-01-25 20:00:12,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:12,732] [INFO] Task started: CheckM
[2024-01-25 20:00:12,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000167975.1_ASM16797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000167975.1_ASM16797v1_genomic.fna/checkm_input GCF_000167975.1_ASM16797v1_genomic.fna/checkm_result
[2024-01-25 20:00:44,369] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:44,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:44,389] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:44,389] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:44,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000167975.1_ASM16797v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:44,390] [INFO] Task started: Blastn
[2024-01-25 20:00:44,390] [INFO] Running command: blastn -query GCF_000167975.1_ASM16797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd248cf96-a2f0-4e63-9a8b-f2e66bbaee50/dqc_reference/reference_markers_gtdb.fasta -out GCF_000167975.1_ASM16797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:45,595] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:45,598] [INFO] Selected 13 target genomes.
[2024-01-25 20:00:45,598] [INFO] Target genome list was writen to GCF_000167975.1_ASM16797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:45,613] [INFO] Task started: fastANI
[2024-01-25 20:00:45,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c6c921-ce9e-47ce-8b9b-5b3f3cf81887/GCF_000167975.1_ASM16797v1_genomic.fna.gz --refList GCF_000167975.1_ASM16797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000167975.1_ASM16797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:59,363] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:59,371] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:59,372] [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_013282745.1	s__Yersinia bercovieri	99.9963	1367	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.12	95.38	0.94	0.87	18	conclusive
GCF_001047675.1	s__Yersinia aleksiciae	91.2949	1036	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_013282725.1	s__Yersinia mollaretii	89.8001	1147	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.95	95.82	0.92	0.88	25	-
GCF_000312485.1	s__Yersinia massiliensis	85.5294	1111	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.58	95.54	0.91	0.88	22	-
GCF_001152565.1	s__Yersinia pekkanenii	84.9928	1008	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_001098625.1	s__Yersinia frederiksenii_C	84.8764	1053	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_001123825.1	s__Yersinia kristensenii_C	84.767	1024	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_001995075.1	s__Yersinia enterocolitica_F	84.7445	1040	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_902726525.1	s__Yersinia enterocolitica_H	84.6783	1025	1369	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	84.5717	1028	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_000754805.1	s__Yersinia frederiksenii	84.5138	1068	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	-
GCF_900460525.1	s__Yersinia kristensenii	84.5116	1018	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_000173775.1	s__Yersinia rohdei	84.1529	998	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.41	99.12	0.94	0.89	12	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:59,373] [INFO] GTDB search result was written to GCF_000167975.1_ASM16797v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:59,373] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:59,376] [INFO] DFAST_QC result json was written to GCF_000167975.1_ASM16797v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:59,377] [INFO] DFAST_QC completed!
[2024-01-25 20:00:59,377] [INFO] Total running time: 0h1m9s