[2024-01-25 19:02:05,485] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:05,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:05,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg4adfc912-20e9-4b87-8069-515dc0783778/dqc_reference
[2024-01-25 19:02:06,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:06,603] [INFO] Task started: Prodigal
[2024-01-25 19:02:06,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg0093db91-4370-49bf-a6b6-23c0198139d8/GCF_017565745.1_ASM1756574v1_genomic.fna.gz | prodigal -d GCF_017565745.1_ASM1756574v1_genomic.fna/cds.fna -a GCF_017565745.1_ASM1756574v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:14,412] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:14,412] [INFO] Task started: HMMsearch
[2024-01-25 19:02:14,412] [INFO] Running command: hmmsearch --tblout GCF_017565745.1_ASM1756574v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4adfc912-20e9-4b87-8069-515dc0783778/dqc_reference/reference_markers.hmm GCF_017565745.1_ASM1756574v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:14,678] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:14,679] [INFO] Found 6/6 markers.
[2024-01-25 19:02:14,706] [INFO] Query marker FASTA was written to GCF_017565745.1_ASM1756574v1_genomic.fna/markers.fasta
[2024-01-25 19:02:14,706] [INFO] Task started: Blastn
[2024-01-25 19:02:14,706] [INFO] Running command: blastn -query GCF_017565745.1_ASM1756574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4adfc912-20e9-4b87-8069-515dc0783778/dqc_reference/reference_markers.fasta -out GCF_017565745.1_ASM1756574v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:15,809] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:15,812] [INFO] Selected 16 target genomes.
[2024-01-25 19:02:15,812] [INFO] Target genome list was writen to GCF_017565745.1_ASM1756574v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:15,837] [INFO] Task started: fastANI
[2024-01-25 19:02:15,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg0093db91-4370-49bf-a6b6-23c0198139d8/GCF_017565745.1_ASM1756574v1_genomic.fna.gz --refList GCF_017565745.1_ASM1756574v1_genomic.fna/target_genomes.txt --output GCF_017565745.1_ASM1756574v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:26,877] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:26,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4adfc912-20e9-4b87-8069-515dc0783778/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:26,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4adfc912-20e9-4b87-8069-515dc0783778/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:26,888] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:26,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:26,888] [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
Leucobacter weissii	strain=S27	GCA_017565745.1	1983706	1983706	type	True	100.0	1106	1108	95	conclusive
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	81.0529	477	1108	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	80.3587	465	1108	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	80.2823	468	1108	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	80.1058	489	1108	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	80.0872	451	1108	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	80.049	458	1108	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	79.9455	435	1108	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	79.8988	425	1108	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	79.8174	455	1108	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	79.7608	425	1108	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.7217	310	1108	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.6919	289	1108	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.4827	261	1108	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	77.2822	214	1108	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	77.2654	216	1108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:26,889] [INFO] DFAST Taxonomy check result was written to GCF_017565745.1_ASM1756574v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:26,890] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:26,890] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:26,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4adfc912-20e9-4b87-8069-515dc0783778/dqc_reference/checkm_data
[2024-01-25 19:02:26,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:26,925] [INFO] Task started: CheckM
[2024-01-25 19:02:26,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017565745.1_ASM1756574v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017565745.1_ASM1756574v1_genomic.fna/checkm_input GCF_017565745.1_ASM1756574v1_genomic.fna/checkm_result
[2024-01-25 19:02:56,396] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:56,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:56,413] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:56,413] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:56,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017565745.1_ASM1756574v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:56,413] [INFO] Task started: Blastn
[2024-01-25 19:02:56,413] [INFO] Running command: blastn -query GCF_017565745.1_ASM1756574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4adfc912-20e9-4b87-8069-515dc0783778/dqc_reference/reference_markers_gtdb.fasta -out GCF_017565745.1_ASM1756574v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:58,318] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:58,321] [INFO] Selected 14 target genomes.
[2024-01-25 19:02:58,322] [INFO] Target genome list was writen to GCF_017565745.1_ASM1756574v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:58,335] [INFO] Task started: fastANI
[2024-01-25 19:02:58,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg0093db91-4370-49bf-a6b6-23c0198139d8/GCF_017565745.1_ASM1756574v1_genomic.fna.gz --refList GCF_017565745.1_ASM1756574v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017565745.1_ASM1756574v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:07,884] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:07,893] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:07,894] [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_017565745.1	s__Leucobacter weissii	100.0	1106	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016771945.1	s__Leucobacter sulfamidivorax	81.322	484	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_910593785.1	s__Leucobacter sp910593785	81.0799	475	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028235.1	s__Leucobacter muris	80.4092	461	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_001273835.1	s__Leucobacter celer	80.0842	491	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569785.1	s__Leucobacter sp003569785	80.0097	479	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565705.1	s__Leucobacter ruminantium	79.9459	435	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102345.1	s__Leucobacter chromiiresistens	79.8483	429	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.76	99.76	0.96	0.96	2	-
GCF_002982315.1	s__Leucobacter massiliensis	79.8338	454	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752355.1	s__Leucobacter sp002752355	79.8226	445	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
GCF_000980875.1	s__Leucobacter sp000980875	79.7384	432	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001477055.1	s__Leucobacter chromiiresistens_A	79.7147	386	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016522535.1	s__Leucobacter sp016522535	79.6116	367	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016758175.1	s__Leucobacter zeae	79.5645	432	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:07,895] [INFO] GTDB search result was written to GCF_017565745.1_ASM1756574v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:07,896] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:07,899] [INFO] DFAST_QC result json was written to GCF_017565745.1_ASM1756574v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:07,899] [INFO] DFAST_QC completed!
[2024-01-25 19:03:07,899] [INFO] Total running time: 0h1m2s