[2024-01-24 13:01:19,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:19,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:19,348] [INFO] DQC Reference Directory: /var/lib/cwl/stgffcaa33c-0436-4816-bd3b-afb93f1c459b/dqc_reference
[2024-01-24 13:01:20,579] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,580] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,580] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8067b5f-10ae-4518-a23c-97cf33cd604c/GCF_000429565.1_ASM42956v1_genomic.fna.gz | prodigal -d GCF_000429565.1_ASM42956v1_genomic.fna/cds.fna -a GCF_000429565.1_ASM42956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:27,055] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:27,056] [INFO] Task started: HMMsearch
[2024-01-24 13:01:27,056] [INFO] Running command: hmmsearch --tblout GCF_000429565.1_ASM42956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffcaa33c-0436-4816-bd3b-afb93f1c459b/dqc_reference/reference_markers.hmm GCF_000429565.1_ASM42956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:27,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:27,312] [INFO] Found 6/6 markers.
[2024-01-24 13:01:27,343] [INFO] Query marker FASTA was written to GCF_000429565.1_ASM42956v1_genomic.fna/markers.fasta
[2024-01-24 13:01:27,344] [INFO] Task started: Blastn
[2024-01-24 13:01:27,344] [INFO] Running command: blastn -query GCF_000429565.1_ASM42956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffcaa33c-0436-4816-bd3b-afb93f1c459b/dqc_reference/reference_markers.fasta -out GCF_000429565.1_ASM42956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:27,991] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:27,995] [INFO] Selected 20 target genomes.
[2024-01-24 13:01:27,996] [INFO] Target genome list was writen to GCF_000429565.1_ASM42956v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:28,011] [INFO] Task started: fastANI
[2024-01-24 13:01:28,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8067b5f-10ae-4518-a23c-97cf33cd604c/GCF_000429565.1_ASM42956v1_genomic.fna.gz --refList GCF_000429565.1_ASM42956v1_genomic.fna/target_genomes.txt --output GCF_000429565.1_ASM42956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:41,847] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:41,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffcaa33c-0436-4816-bd3b-afb93f1c459b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:41,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffcaa33c-0436-4816-bd3b-afb93f1c459b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:41,873] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:41,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:41,873] [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
Arsenophonus nasoniae	strain=DSM 15247	GCA_000429565.1	638	638	type	True	100.0	1070	1078	95	conclusive
Arsenophonus apicola	strain=ArsBeeUS	GCA_020268605.1	2879119	2879119	type	True	92.1653	920	1078	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	78.2957	52	1078	95	below_threshold
Photorhabdus asymbiotica	strain=DSM 15149	GCA_003634575.1	291112	291112	type	True	78.0898	115	1078	95	below_threshold
Photorhabdus aegyptia	strain=BA1	GCA_000612035.1	2805098	2805098	type	True	77.8866	102	1078	95	below_threshold
Xenorhabdus szentirmaii	strain=DSM 16338	GCA_002632585.1	290112	290112	type	True	77.8284	112	1078	95	below_threshold
Xenorhabdus szentirmaii	strain=DSM 16338	GCA_000531455.1	290112	290112	type	True	77.7663	106	1078	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	77.7023	60	1078	95	below_threshold
Photorhabdus heterorhabditis	strain=SF41	GCA_018448905.1	880156	880156	type	True	77.6929	124	1078	95	below_threshold
Photorhabdus heterorhabditis subsp. aluminescens	strain=Q614	GCA_013277735.1	2805094	880156	type	True	77.524	130	1078	95	below_threshold
Proteus mirabilis	strain=ATCC 29906	GCA_000160755.1	584	584	type	True	77.4959	142	1078	95	below_threshold
Providencia huaxiensis	strain=WCHPr000369	GCA_002843235.3	2027290	2027290	type	True	77.3936	143	1078	95	below_threshold
Moellerella wisconsensis	strain=NCTC12132	GCA_900706815.1	158849	158849	type	True	77.3755	153	1078	95	below_threshold
Moellerella wisconsensis	strain=ATCC 35017	GCA_001294465.1	158849	158849	type	True	77.1661	149	1078	95	below_threshold
Providencia burhodogranariea	strain=DSM 19968	GCA_000314855.2	516074	516074	type	True	77.1361	145	1078	95	below_threshold
Providencia sneebia	strain=DSM 19967	GCA_000314895.2	516075	516075	type	True	77.1146	139	1078	95	below_threshold
Proteus myxofaciens	strain=ATCC 19692	GCA_001654855.1	184072	184072	type	True	77.0271	144	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:41,875] [INFO] DFAST Taxonomy check result was written to GCF_000429565.1_ASM42956v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:41,876] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:41,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:41,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffcaa33c-0436-4816-bd3b-afb93f1c459b/dqc_reference/checkm_data
[2024-01-24 13:01:41,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:41,919] [INFO] Task started: CheckM
[2024-01-24 13:01:41,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429565.1_ASM42956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429565.1_ASM42956v1_genomic.fna/checkm_input GCF_000429565.1_ASM42956v1_genomic.fna/checkm_result
[2024-01-24 13:02:07,399] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:07,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:07,424] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:07,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:07,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429565.1_ASM42956v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:07,425] [INFO] Task started: Blastn
[2024-01-24 13:02:07,425] [INFO] Running command: blastn -query GCF_000429565.1_ASM42956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffcaa33c-0436-4816-bd3b-afb93f1c459b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429565.1_ASM42956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:08,228] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:08,234] [INFO] Selected 7 target genomes.
[2024-01-24 13:02:08,234] [INFO] Target genome list was writen to GCF_000429565.1_ASM42956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:08,243] [INFO] Task started: fastANI
[2024-01-24 13:02:08,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8067b5f-10ae-4518-a23c-97cf33cd604c/GCF_000429565.1_ASM42956v1_genomic.fna.gz --refList GCF_000429565.1_ASM42956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429565.1_ASM42956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:13,174] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:13,184] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:13,184] [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_000429565.1	s__Arsenophonus nasoniae	100.0	1070	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Arsenophonus	95.0	99.85	99.85	0.98	0.98	2	conclusive
GCF_903968575.1	s__Arsenophonus sp903968575	92.2832	909	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Arsenophonus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013460135.1	s__Arsenophonus sp000757905	88.6871	654	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Arsenophonus	95.0	96.52	95.82	0.74	0.66	3	-
GCF_902713415.1	s__Arsenophonus sp902713415	88.4502	406	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Arsenophonus	95.0	95.88	95.88	0.82	0.82	2	-
GCF_900343025.1	s__Arsenophonus sp900343025	87.8914	785	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Arsenophonus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640365.1	s__Arsenophonus triatominarum	87.7366	538	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Arsenophonus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900343015.1	s__Arsenophonus sp900343015	82.7198	195	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Arsenophonus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:13,191] [INFO] GTDB search result was written to GCF_000429565.1_ASM42956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:13,192] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:13,195] [INFO] DFAST_QC result json was written to GCF_000429565.1_ASM42956v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:13,195] [INFO] DFAST_QC completed!
[2024-01-24 13:02:13,195] [INFO] Total running time: 0h0m54s