[2024-01-24 14:28:02,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c416a2e-a824-4bc0-bab8-249ff2f8b5a6/dqc_reference
[2024-01-24 14:28:04,077] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:04,078] [INFO] Task started: Prodigal
[2024-01-24 14:28:04,078] [INFO] Running command: gunzip -c /var/lib/cwl/stg805fe515-91d3-49cd-9446-841915157bcf/GCF_001976145.1_ASM197614v1_genomic.fna.gz | prodigal -d GCF_001976145.1_ASM197614v1_genomic.fna/cds.fna -a GCF_001976145.1_ASM197614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:18,950] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:18,950] [INFO] Task started: HMMsearch
[2024-01-24 14:28:18,950] [INFO] Running command: hmmsearch --tblout GCF_001976145.1_ASM197614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c416a2e-a824-4bc0-bab8-249ff2f8b5a6/dqc_reference/reference_markers.hmm GCF_001976145.1_ASM197614v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:19,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:19,367] [INFO] Found 6/6 markers.
[2024-01-24 14:28:19,409] [INFO] Query marker FASTA was written to GCF_001976145.1_ASM197614v1_genomic.fna/markers.fasta
[2024-01-24 14:28:19,410] [INFO] Task started: Blastn
[2024-01-24 14:28:19,410] [INFO] Running command: blastn -query GCF_001976145.1_ASM197614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c416a2e-a824-4bc0-bab8-249ff2f8b5a6/dqc_reference/reference_markers.fasta -out GCF_001976145.1_ASM197614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:20,306] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:20,310] [INFO] Selected 24 target genomes.
[2024-01-24 14:28:20,310] [INFO] Target genome list was writen to GCF_001976145.1_ASM197614v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:20,331] [INFO] Task started: fastANI
[2024-01-24 14:28:20,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg805fe515-91d3-49cd-9446-841915157bcf/GCF_001976145.1_ASM197614v1_genomic.fna.gz --refList GCF_001976145.1_ASM197614v1_genomic.fna/target_genomes.txt --output GCF_001976145.1_ASM197614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:47,671] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:47,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c416a2e-a824-4bc0-bab8-249ff2f8b5a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:47,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c416a2e-a824-4bc0-bab8-249ff2f8b5a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:47,691] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:28:47,691] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:28:47,692] [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
Chania multitudinisentens	strain=RB-25	GCA_000568195.1	1639108	1639108	type	True	84.1569	1111	1641	95	below_threshold
Chania multitudinisentens	strain=RB-25	GCA_000520015.2	1639108	1639108	type	True	84.0821	1134	1641	95	below_threshold
Serratia fonticola	strain=LMG 7882	GCA_000469035.1	47917	47917	suspected-type	True	83.4328	978	1641	95	below_threshold
Serratia fonticola	strain=DSM 4576	GCA_001006005.1	47917	47917	suspected-type	True	83.3985	1040	1641	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	82.9099	893	1641	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	82.6638	914	1641	95	below_threshold
Serratia liquefaciens	strain=ATCC 27592	GCA_000422085.1	614	614	type	True	82.5696	899	1641	95	below_threshold
Serratia proteamaculans	strain=CCUG 14510	GCA_008830365.1	28151	28151	type	True	82.4398	900	1641	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	82.368	901	1641	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	82.3458	912	1641	95	below_threshold
Serratia ureilytica	strain=CCUG:50595	GCA_013375155.1	300181	300181	type	True	82.3004	895	1641	95	below_threshold
Serratia quinivorans	strain=NCTC11544	GCA_900457075.1	137545	137545	suspected-type	True	82.265	924	1641	95	below_threshold
Serratia surfactantfaciens	strain=YD25	GCA_001642805.2	2741499	2741499	type	True	82.2489	899	1641	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	82.2167	877	1641	95	below_threshold
Serratia odorifera	strain=NCTC11214	GCA_900635445.1	618	618	type	True	81.8431	832	1641	95	below_threshold
Serratia grimesii	strain=NCTC11543	GCA_900456935.1	82995	82995	type	True	81.6723	858	1641	95	below_threshold
Serratia grimesii	strain=NBRC 13537	GCA_001590905.1	82995	82995	type	True	81.6666	840	1641	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	79.1205	486	1641	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	79.079	439	1641	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	78.573	433	1641	95	below_threshold
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	78.2558	450	1641	95	below_threshold
Photorhabdus heterorhabditis subsp. aluminescens	strain=Q614	GCA_013277735.1	2805094	880156	type	True	78.0636	145	1641	95	below_threshold
Sodalis ligni	strain=159R	GCA_004346745.1	2697027	2697027	type	True	77.5335	329	1641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:47,694] [INFO] DFAST Taxonomy check result was written to GCF_001976145.1_ASM197614v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:47,694] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:47,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:47,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c416a2e-a824-4bc0-bab8-249ff2f8b5a6/dqc_reference/checkm_data
[2024-01-24 14:28:47,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:47,746] [INFO] Task started: CheckM
[2024-01-24 14:28:47,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001976145.1_ASM197614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001976145.1_ASM197614v1_genomic.fna/checkm_input GCF_001976145.1_ASM197614v1_genomic.fna/checkm_result
[2024-01-24 14:29:33,896] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:33,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:33,928] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:33,928] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:33,929] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001976145.1_ASM197614v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:33,929] [INFO] Task started: Blastn
[2024-01-24 14:29:33,929] [INFO] Running command: blastn -query GCF_001976145.1_ASM197614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c416a2e-a824-4bc0-bab8-249ff2f8b5a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001976145.1_ASM197614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:35,089] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:35,092] [INFO] Selected 15 target genomes.
[2024-01-24 14:29:35,092] [INFO] Target genome list was writen to GCF_001976145.1_ASM197614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:35,112] [INFO] Task started: fastANI
[2024-01-24 14:29:35,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg805fe515-91d3-49cd-9446-841915157bcf/GCF_001976145.1_ASM197614v1_genomic.fna.gz --refList GCF_001976145.1_ASM197614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001976145.1_ASM197614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:52,596] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:52,615] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:52,615] [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_001976145.1	s__Chania oryzae	100.0	1641	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	conclusive
GCF_000743355.1	s__Chania sp000743355	86.8278	1277	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000520015.2	s__Chania multitudinisentens	84.1013	1131	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001006005.1	s__Serratia_A fonticola	83.394	1041	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	96.10	95.03	0.87	0.81	45	-
GCF_000633355.1	s__Serratia_A sp000633355	83.3166	1030	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715025.1	s__Serratia_A fonticola_A	83.1265	1028	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	4	-
GCF_018336935.1	s__Serratia plymuthica_B	82.7548	915	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422085.1	s__Serratia liquefaciens	82.5601	899	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.63	98.20	0.94	0.91	25	-
GCF_016742975.1	s__Serratia nevei	82.3789	805	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_002220655.1	s__Serratia marcescens_K	82.343	920	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_006715005.1	s__Serratia marcescens_J	82.2922	899	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_001642805.2	s__Serratia surfactantfaciens	82.2489	899	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_000496755.2	s__Serratia_A sp000496755	80.1043	697	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831415.1	s__Yersinia canariae	79.3122	445	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
GCF_000770305.1	s__Erwinia oleae	78.2004	366	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.06	98.06	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:52,617] [INFO] GTDB search result was written to GCF_001976145.1_ASM197614v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:52,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:52,621] [INFO] DFAST_QC result json was written to GCF_001976145.1_ASM197614v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:52,621] [INFO] DFAST_QC completed!
[2024-01-24 14:29:52,622] [INFO] Total running time: 0h1m50s