[2024-01-24 15:27:12,736] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a09bc7b-ac13-464c-b85a-08882a79f902/dqc_reference
[2024-01-24 15:27:14,116] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:14,117] [INFO] Task started: Prodigal
[2024-01-24 15:27:14,117] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e2306de-7f42-43d9-a540-026f93cca966/GCF_016522505.1_ASM1652250v1_genomic.fna.gz | prodigal -d GCF_016522505.1_ASM1652250v1_genomic.fna/cds.fna -a GCF_016522505.1_ASM1652250v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:23,135] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:23,136] [INFO] Task started: HMMsearch
[2024-01-24 15:27:23,136] [INFO] Running command: hmmsearch --tblout GCF_016522505.1_ASM1652250v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a09bc7b-ac13-464c-b85a-08882a79f902/dqc_reference/reference_markers.hmm GCF_016522505.1_ASM1652250v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:23,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:23,433] [INFO] Found 6/6 markers.
[2024-01-24 15:27:23,490] [INFO] Query marker FASTA was written to GCF_016522505.1_ASM1652250v1_genomic.fna/markers.fasta
[2024-01-24 15:27:23,491] [INFO] Task started: Blastn
[2024-01-24 15:27:23,491] [INFO] Running command: blastn -query GCF_016522505.1_ASM1652250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a09bc7b-ac13-464c-b85a-08882a79f902/dqc_reference/reference_markers.fasta -out GCF_016522505.1_ASM1652250v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:24,841] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:24,846] [INFO] Selected 14 target genomes.
[2024-01-24 15:27:24,847] [INFO] Target genome list was writen to GCF_016522505.1_ASM1652250v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:24,852] [INFO] Task started: fastANI
[2024-01-24 15:27:24,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e2306de-7f42-43d9-a540-026f93cca966/GCF_016522505.1_ASM1652250v1_genomic.fna.gz --refList GCF_016522505.1_ASM1652250v1_genomic.fna/target_genomes.txt --output GCF_016522505.1_ASM1652250v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:35,438] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:35,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a09bc7b-ac13-464c-b85a-08882a79f902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:35,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a09bc7b-ac13-464c-b85a-08882a79f902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:35,457] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:35,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:35,458] [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 chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	100.0	1092	1096	95	conclusive
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	82.4709	558	1096	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	82.0201	566	1096	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	81.6863	568	1096	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	81.4676	575	1096	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	81.4118	532	1096	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	81.3815	549	1096	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	81.2365	536	1096	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	81.1592	499	1096	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	80.9836	452	1096	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.4538	340	1096	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3685	389	1096	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	77.762	287	1096	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.5641	272	1096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:35,460] [INFO] DFAST Taxonomy check result was written to GCF_016522505.1_ASM1652250v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:35,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:35,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:35,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a09bc7b-ac13-464c-b85a-08882a79f902/dqc_reference/checkm_data
[2024-01-24 15:27:35,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:35,498] [INFO] Task started: CheckM
[2024-01-24 15:27:35,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016522505.1_ASM1652250v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016522505.1_ASM1652250v1_genomic.fna/checkm_input GCF_016522505.1_ASM1652250v1_genomic.fna/checkm_result
[2024-01-24 15:28:07,522] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:07,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:07,543] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:07,543] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:07,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016522505.1_ASM1652250v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:07,544] [INFO] Task started: Blastn
[2024-01-24 15:28:07,544] [INFO] Running command: blastn -query GCF_016522505.1_ASM1652250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a09bc7b-ac13-464c-b85a-08882a79f902/dqc_reference/reference_markers_gtdb.fasta -out GCF_016522505.1_ASM1652250v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:09,381] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:09,385] [INFO] Selected 14 target genomes.
[2024-01-24 15:28:09,385] [INFO] Target genome list was writen to GCF_016522505.1_ASM1652250v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:09,398] [INFO] Task started: fastANI
[2024-01-24 15:28:09,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e2306de-7f42-43d9-a540-026f93cca966/GCF_016522505.1_ASM1652250v1_genomic.fna.gz --refList GCF_016522505.1_ASM1652250v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016522505.1_ASM1652250v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:19,917] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:19,941] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:19,942] [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_016522505.1	s__Leucobacter sp016522505	100.0	1092	1096	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_000421845.1	s__Leucobacter chironomi	82.4626	558	1096	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	81.9809	570	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_017565705.1	s__Leucobacter ruminantium	81.7238	565	1096	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	81.4556	488	1096	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	81.4548	576	1096	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	81.3241	577	1096	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	81.1695	513	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
GCF_001477055.1	s__Leucobacter chromiiresistens_A	81.1278	457	1096	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	81.1254	502	1096	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	81.105	498	1096	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	80.9715	515	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003917135.1	s__Leucobacter chromiireducens_A	80.7798	489	1096	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	80.6413	446	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:19,943] [INFO] GTDB search result was written to GCF_016522505.1_ASM1652250v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:19,946] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:19,950] [INFO] DFAST_QC result json was written to GCF_016522505.1_ASM1652250v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:19,950] [INFO] DFAST_QC completed!
[2024-01-24 15:28:19,950] [INFO] Total running time: 0h1m7s