[2024-01-24 13:09:51,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,506] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b1c36b0-ceef-4929-8c96-8a6baabfe30f/dqc_reference
[2024-01-24 13:09:52,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:52,995] [INFO] Task started: Prodigal
[2024-01-24 13:09:52,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg01e5568f-0114-4d25-8695-b37c5c0db756/GCF_900460425.1_28307_B01_genomic.fna.gz | prodigal -d GCF_900460425.1_28307_B01_genomic.fna/cds.fna -a GCF_900460425.1_28307_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:06,715] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:06,715] [INFO] Task started: HMMsearch
[2024-01-24 13:10:06,716] [INFO] Running command: hmmsearch --tblout GCF_900460425.1_28307_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b1c36b0-ceef-4929-8c96-8a6baabfe30f/dqc_reference/reference_markers.hmm GCF_900460425.1_28307_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:07,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:07,044] [INFO] Found 6/6 markers.
[2024-01-24 13:10:07,093] [INFO] Query marker FASTA was written to GCF_900460425.1_28307_B01_genomic.fna/markers.fasta
[2024-01-24 13:10:07,093] [INFO] Task started: Blastn
[2024-01-24 13:10:07,093] [INFO] Running command: blastn -query GCF_900460425.1_28307_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b1c36b0-ceef-4929-8c96-8a6baabfe30f/dqc_reference/reference_markers.fasta -out GCF_900460425.1_28307_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:07,867] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:07,870] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:07,870] [INFO] Target genome list was writen to GCF_900460425.1_28307_B01_genomic.fna/target_genomes.txt
[2024-01-24 13:10:07,875] [INFO] Task started: fastANI
[2024-01-24 13:10:07,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg01e5568f-0114-4d25-8695-b37c5c0db756/GCF_900460425.1_28307_B01_genomic.fna.gz --refList GCF_900460425.1_28307_B01_genomic.fna/target_genomes.txt --output GCF_900460425.1_28307_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:21,897] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:21,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b1c36b0-ceef-4929-8c96-8a6baabfe30f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:21,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b1c36b0-ceef-4929-8c96-8a6baabfe30f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:21,909] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:10:21,910] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:21,910] [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 frederiksenii	strain=NCTC11470	GCA_900460425.1	29484	29484	suspected-type	True	100.0	1664	1667	95	conclusive
Yersinia frederiksenii	strain=ATCC 33641	GCA_000754805.1	29484	29484	suspected-type	True	99.9927	1638	1667	95	conclusive
Yersinia frederiksenii	strain=ATCC 33641	GCA_000168015.1	29484	29484	suspected-type	True	99.9594	1575	1667	95	conclusive
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	92.1451	1388	1667	95	below_threshold
Yersinia vastinensis	strain=IP38594	GCA_902726565.1	2890318	2890318	type	True	87.1653	1229	1667	95	below_threshold
Yersinia proxima	strain=IP37424	GCA_902170785.1	2890316	2890316	type	True	85.4397	1176	1667	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	83.8262	1046	1667	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.7248	383	1667	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.2313	373	1667	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.0756	371	1667	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	78.4497	269	1667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:21,916] [INFO] DFAST Taxonomy check result was written to GCF_900460425.1_28307_B01_genomic.fna/tc_result.tsv
[2024-01-24 13:10:21,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:21,919] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:21,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b1c36b0-ceef-4929-8c96-8a6baabfe30f/dqc_reference/checkm_data
[2024-01-24 13:10:21,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:21,973] [INFO] Task started: CheckM
[2024-01-24 13:10:21,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460425.1_28307_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460425.1_28307_B01_genomic.fna/checkm_input GCF_900460425.1_28307_B01_genomic.fna/checkm_result
[2024-01-24 13:11:06,149] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:06,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:06,169] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:06,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:06,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460425.1_28307_B01_genomic.fna/markers.fasta)
[2024-01-24 13:11:06,170] [INFO] Task started: Blastn
[2024-01-24 13:11:06,170] [INFO] Running command: blastn -query GCF_900460425.1_28307_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b1c36b0-ceef-4929-8c96-8a6baabfe30f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460425.1_28307_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:07,138] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:07,142] [INFO] Selected 16 target genomes.
[2024-01-24 13:11:07,143] [INFO] Target genome list was writen to GCF_900460425.1_28307_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:07,154] [INFO] Task started: fastANI
[2024-01-24 13:11:07,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg01e5568f-0114-4d25-8695-b37c5c0db756/GCF_900460425.1_28307_B01_genomic.fna.gz --refList GCF_900460425.1_28307_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460425.1_28307_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:26,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:26,271] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:26,271] [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_000754805.1	s__Yersinia frederiksenii	99.9927	1638	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	conclusive
GCF_001098625.1	s__Yersinia frederiksenii_C	92.1764	1409	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_001155565.1	s__Yersinia frederiksenii_A	86.9757	1276	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.53	99.44	0.95	0.92	10	-
GCF_000173775.1	s__Yersinia rohdei	85.8947	1149	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.41	99.12	0.94	0.89	12	-
GCF_009831415.1	s__Yersinia canariae	85.7646	1258	1667	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	85.6643	1220	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_901472495.1	s__Yersinia enterocolitica	85.5061	1173	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_001123825.1	s__Yersinia kristensenii_C	85.4686	1133	1667	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	85.4533	1169	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_900460525.1	s__Yersinia kristensenii	85.4285	1198	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_003600645.1	s__Yersinia rochesterensis	85.3986	1182	1667	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	85.2997	1186	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_001047675.1	s__Yersinia aleksiciae	85.0338	1037	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_002858675.1	s__Chimaeribacter californicus	79.1124	305	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chimaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141005.1	s__Erwinia sp001422605	78.8733	222	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.39	98.36	0.92	0.92	3	-
GCF_900068835.1	s__Pantoea ludwigii_B	78.321	227	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.17	96.60	0.91	0.89	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:26,273] [INFO] GTDB search result was written to GCF_900460425.1_28307_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:26,273] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:26,278] [INFO] DFAST_QC result json was written to GCF_900460425.1_28307_B01_genomic.fna/dqc_result.json
[2024-01-24 13:11:26,278] [INFO] DFAST_QC completed!
[2024-01-24 13:11:26,278] [INFO] Total running time: 0h1m35s