[2024-01-25 20:12:05,415] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ab4751a-a487-4112-9f9d-38240d5c470e/dqc_reference
[2024-01-25 20:12:06,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:06,568] [INFO] Task started: Prodigal
[2024-01-25 20:12:06,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg9feba2c7-74f8-4d2b-9488-19238c9f40eb/GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/cds.fna -a GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:14,513] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:14,513] [INFO] Task started: HMMsearch
[2024-01-25 20:12:14,513] [INFO] Running command: hmmsearch --tblout GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ab4751a-a487-4112-9f9d-38240d5c470e/dqc_reference/reference_markers.hmm GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:14,734] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:14,735] [INFO] Found 6/6 markers.
[2024-01-25 20:12:14,762] [INFO] Query marker FASTA was written to GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:12:14,762] [INFO] Task started: Blastn
[2024-01-25 20:12:14,762] [INFO] Running command: blastn -query GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab4751a-a487-4112-9f9d-38240d5c470e/dqc_reference/reference_markers.fasta -out GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:15,308] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:15,310] [INFO] Selected 19 target genomes.
[2024-01-25 20:12:15,311] [INFO] Target genome list was writen to GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:12:15,329] [INFO] Task started: fastANI
[2024-01-25 20:12:15,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg9feba2c7-74f8-4d2b-9488-19238c9f40eb/GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna.gz --refList GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:27,915] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:27,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ab4751a-a487-4112-9f9d-38240d5c470e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:27,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ab4751a-a487-4112-9f9d-38240d5c470e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:27,923] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:27,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:27,924] [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
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	100.0	1206	1208	95	conclusive
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	78.6813	464	1208	95	below_threshold
Lentibacillus jeotgali	strain=Grbi	GCA_000224785.2	558169	558169	type	True	78.6573	493	1208	95	below_threshold
Lentibacillus kapialis	strain=JCM 12580	GCA_014646635.1	340214	340214	type	True	78.4927	364	1208	95	below_threshold
Lentibacillus persicus	strain=DSM 22530	GCA_900112705.1	640948	640948	type	True	77.9128	342	1208	95	below_threshold
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	77.8406	263	1208	95	below_threshold
Lentibacillus cibarius	strain=NKC220-2	GCA_005887555.1	2583219	2583219	type	True	77.3724	249	1208	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	77.0971	171	1208	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	77.0926	67	1208	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	77.0779	175	1208	95	below_threshold
Lentibacillus saliphilus	strain=YIM 93176	GCA_019093865.1	2737028	2737028	type	True	76.7094	58	1208	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:27,925] [INFO] DFAST Taxonomy check result was written to GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:12:27,925] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:27,926] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:27,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ab4751a-a487-4112-9f9d-38240d5c470e/dqc_reference/checkm_data
[2024-01-25 20:12:27,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:27,963] [INFO] Task started: CheckM
[2024-01-25 20:12:27,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/checkm_input GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:12:55,909] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:55,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:55,933] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:55,934] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:55,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:12:55,934] [INFO] Task started: Blastn
[2024-01-25 20:12:55,934] [INFO] Running command: blastn -query GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab4751a-a487-4112-9f9d-38240d5c470e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:56,725] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:56,729] [INFO] Selected 14 target genomes.
[2024-01-25 20:12:56,729] [INFO] Target genome list was writen to GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:56,745] [INFO] Task started: fastANI
[2024-01-25 20:12:56,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg9feba2c7-74f8-4d2b-9488-19238c9f40eb/GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna.gz --refList GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:07,119] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:07,129] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:07,130] [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_900112045.1	s__Lentibacillus halodurans	100.0	1206	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013373365.1	s__Lentibacillus sp013373365	79.8588	627	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004565465.1	s__Lentibacillus salicampi	79.1093	490	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307805.1	s__Lentibacillus amyloliquefaciens	78.6719	464	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224785.1	s__Lentibacillus jeotgali	78.6647	493	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646635.1	s__Lentibacillus kapialis	78.4927	364	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112705.1	s__Lentibacillus persicus	77.9308	339	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902806455.1	s__Lentibacillus doumboii	77.8406	263	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004145795.1	s__Lentibacillus lipolyticus	77.7005	252	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001311805.1	s__Lentibacillus juripiscarius	77.6698	270	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110695.1	s__Lentibacillus subterraneus	77.1121	170	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_017873675.1	s__Lentibacillus litoralis	77.0782	176	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908155.1	s__Oceanobacillus caeni	76.9159	60	1208	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:07,131] [INFO] GTDB search result was written to GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:07,132] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:07,135] [INFO] DFAST_QC result json was written to GCF_900112045.1_IMG-taxon_2617270778_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:13:07,135] [INFO] DFAST_QC completed!
[2024-01-25 20:13:07,136] [INFO] Total running time: 0h1m2s