[2024-01-24 11:12:28,117] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,120] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,120] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf6c53dc-e119-4e23-a3bb-f4d1c67ee47c/dqc_reference
[2024-01-24 11:12:29,450] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,451] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,451] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7baf7db-e113-4eef-8812-fc139ff62b2f/GCF_017583045.1_ASM1758304v1_genomic.fna.gz | prodigal -d GCF_017583045.1_ASM1758304v1_genomic.fna/cds.fna -a GCF_017583045.1_ASM1758304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:38,481] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:38,481] [INFO] Task started: HMMsearch
[2024-01-24 11:12:38,481] [INFO] Running command: hmmsearch --tblout GCF_017583045.1_ASM1758304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf6c53dc-e119-4e23-a3bb-f4d1c67ee47c/dqc_reference/reference_markers.hmm GCF_017583045.1_ASM1758304v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:38,805] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:38,806] [INFO] Found 6/6 markers.
[2024-01-24 11:12:38,841] [INFO] Query marker FASTA was written to GCF_017583045.1_ASM1758304v1_genomic.fna/markers.fasta
[2024-01-24 11:12:38,842] [INFO] Task started: Blastn
[2024-01-24 11:12:38,842] [INFO] Running command: blastn -query GCF_017583045.1_ASM1758304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf6c53dc-e119-4e23-a3bb-f4d1c67ee47c/dqc_reference/reference_markers.fasta -out GCF_017583045.1_ASM1758304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:39,841] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:39,844] [INFO] Selected 17 target genomes.
[2024-01-24 11:12:39,844] [INFO] Target genome list was writen to GCF_017583045.1_ASM1758304v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:39,865] [INFO] Task started: fastANI
[2024-01-24 11:12:39,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7baf7db-e113-4eef-8812-fc139ff62b2f/GCF_017583045.1_ASM1758304v1_genomic.fna.gz --refList GCF_017583045.1_ASM1758304v1_genomic.fna/target_genomes.txt --output GCF_017583045.1_ASM1758304v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:51,893] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:51,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf6c53dc-e119-4e23-a3bb-f4d1c67ee47c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:51,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf6c53dc-e119-4e23-a3bb-f4d1c67ee47c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:51,908] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:51,908] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:51,908] [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 tardus	strain=K 70/01	GCA_017583045.1	501483	501483	type	True	100.0	979	981	95	conclusive
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	80.014	427	981	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	79.9387	400	981	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	79.8553	435	981	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	79.804	436	981	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	79.7681	431	981	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	79.7673	402	981	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	79.5512	421	981	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	79.4936	391	981	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	79.415	350	981	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	79.3975	448	981	95	below_threshold
Leucobacter aridicollis	strain=DSM 17380	GCA_013409595.1	283878	283878	type	True	78.7275	346	981	95	below_threshold
Leucobacter aridicollis	strain=L-9	GCA_016758215.1	283878	283878	type	True	78.6646	337	981	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.613	288	981	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	77.559	257	981	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	77.5062	205	981	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	77.429	245	981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:51,910] [INFO] DFAST Taxonomy check result was written to GCF_017583045.1_ASM1758304v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:51,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:51,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:51,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf6c53dc-e119-4e23-a3bb-f4d1c67ee47c/dqc_reference/checkm_data
[2024-01-24 11:12:51,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:51,943] [INFO] Task started: CheckM
[2024-01-24 11:12:51,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017583045.1_ASM1758304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017583045.1_ASM1758304v1_genomic.fna/checkm_input GCF_017583045.1_ASM1758304v1_genomic.fna/checkm_result
[2024-01-24 11:13:38,077] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:38,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:38,101] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:38,102] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:38,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017583045.1_ASM1758304v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:38,103] [INFO] Task started: Blastn
[2024-01-24 11:13:38,103] [INFO] Running command: blastn -query GCF_017583045.1_ASM1758304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf6c53dc-e119-4e23-a3bb-f4d1c67ee47c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017583045.1_ASM1758304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:39,567] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:39,571] [INFO] Selected 17 target genomes.
[2024-01-24 11:13:39,571] [INFO] Target genome list was writen to GCF_017583045.1_ASM1758304v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:39,599] [INFO] Task started: fastANI
[2024-01-24 11:13:39,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7baf7db-e113-4eef-8812-fc139ff62b2f/GCF_017583045.1_ASM1758304v1_genomic.fna.gz --refList GCF_017583045.1_ASM1758304v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017583045.1_ASM1758304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:50,615] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:50,628] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:50,629] [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_017583045.1	s__Leucobacter tardus	100.0	979	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900102345.1	s__Leucobacter chromiiresistens	79.8553	435	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.76	99.76	0.96	0.96	2	-
GCF_004028235.1	s__Leucobacter muris	79.8053	428	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_000421845.1	s__Leucobacter chironomi	79.7895	401	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016522505.1	s__Leucobacter sp016522505	79.7805	438	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633415.1	s__Leucobacter sp000633415	79.6709	401	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980875.1	s__Leucobacter sp000980875	79.5881	386	981	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	79.5794	413	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
GCF_004208635.1	s__Leucobacter triazinivorans	79.5751	419	981	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	79.5599	434	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982315.1	s__Leucobacter massiliensis	79.5063	390	981	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	79.4426	348	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016771945.1	s__Leucobacter sulfamidivorax	79.429	385	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273835.1	s__Leucobacter celer	79.3981	448	981	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	79.3767	438	981	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	79.3386	359	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016597785.1	s__Leucobacter sp001373475	79.2788	380	981	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.62	98.46	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:50,631] [INFO] GTDB search result was written to GCF_017583045.1_ASM1758304v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:50,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:50,636] [INFO] DFAST_QC result json was written to GCF_017583045.1_ASM1758304v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:50,636] [INFO] DFAST_QC completed!
[2024-01-24 11:13:50,636] [INFO] Total running time: 0h1m23s