[2024-01-24 13:17:34,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg6304d797-e258-4f0f-8a82-b04ffb38fd42/dqc_reference
[2024-01-24 13:17:35,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,692] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,693] [INFO] Running command: gunzip -c /var/lib/cwl/stg45811c9c-316b-432e-966b-774f926d419d/GCF_004208635.1_ASM420863v1_genomic.fna.gz | prodigal -d GCF_004208635.1_ASM420863v1_genomic.fna/cds.fna -a GCF_004208635.1_ASM420863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:46,336] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:46,336] [INFO] Task started: HMMsearch
[2024-01-24 13:17:46,336] [INFO] Running command: hmmsearch --tblout GCF_004208635.1_ASM420863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6304d797-e258-4f0f-8a82-b04ffb38fd42/dqc_reference/reference_markers.hmm GCF_004208635.1_ASM420863v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:46,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:46,630] [INFO] Found 6/6 markers.
[2024-01-24 13:17:46,677] [INFO] Query marker FASTA was written to GCF_004208635.1_ASM420863v1_genomic.fna/markers.fasta
[2024-01-24 13:17:46,678] [INFO] Task started: Blastn
[2024-01-24 13:17:46,678] [INFO] Running command: blastn -query GCF_004208635.1_ASM420863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6304d797-e258-4f0f-8a82-b04ffb38fd42/dqc_reference/reference_markers.fasta -out GCF_004208635.1_ASM420863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:47,715] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:47,719] [INFO] Selected 13 target genomes.
[2024-01-24 13:17:47,719] [INFO] Target genome list was writen to GCF_004208635.1_ASM420863v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:47,724] [INFO] Task started: fastANI
[2024-01-24 13:17:47,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg45811c9c-316b-432e-966b-774f926d419d/GCF_004208635.1_ASM420863v1_genomic.fna.gz --refList GCF_004208635.1_ASM420863v1_genomic.fna/target_genomes.txt --output GCF_004208635.1_ASM420863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:57,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:57,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6304d797-e258-4f0f-8a82-b04ffb38fd42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:57,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6304d797-e258-4f0f-8a82-b04ffb38fd42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:57,530] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:57,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:57,531] [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 triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	100.0	1155	1159	95	conclusive
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	86.383	826	1159	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	83.2491	615	1159	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	83.1439	672	1159	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	82.4388	593	1159	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	82.0242	559	1159	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	81.6852	591	1159	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	81.6346	624	1159	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	80.7783	489	1159	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.9229	358	1159	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.8828	292	1159	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	77.7772	316	1159	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.5657	265	1159	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:57,532] [INFO] DFAST Taxonomy check result was written to GCF_004208635.1_ASM420863v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:57,533] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:57,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:57,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6304d797-e258-4f0f-8a82-b04ffb38fd42/dqc_reference/checkm_data
[2024-01-24 13:17:57,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:57,570] [INFO] Task started: CheckM
[2024-01-24 13:17:57,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004208635.1_ASM420863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004208635.1_ASM420863v1_genomic.fna/checkm_input GCF_004208635.1_ASM420863v1_genomic.fna/checkm_result
[2024-01-24 13:18:35,934] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:35,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:35,954] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:35,955] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:35,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004208635.1_ASM420863v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:35,956] [INFO] Task started: Blastn
[2024-01-24 13:18:35,956] [INFO] Running command: blastn -query GCF_004208635.1_ASM420863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6304d797-e258-4f0f-8a82-b04ffb38fd42/dqc_reference/reference_markers_gtdb.fasta -out GCF_004208635.1_ASM420863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:37,591] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:37,595] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:37,595] [INFO] Target genome list was writen to GCF_004208635.1_ASM420863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:37,604] [INFO] Task started: fastANI
[2024-01-24 13:18:37,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg45811c9c-316b-432e-966b-774f926d419d/GCF_004208635.1_ASM420863v1_genomic.fna.gz --refList GCF_004208635.1_ASM420863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004208635.1_ASM420863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:45,437] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:45,449] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:45,450] [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_004208635.1	s__Leucobacter triazinivorans	100.0	1157	1159	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_001273835.1	s__Leucobacter celer	86.3686	827	1159	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	83.8395	678	1159	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421845.1	s__Leucobacter chironomi	83.219	617	1159	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	83.1697	670	1159	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_002982315.1	s__Leucobacter massiliensis	82.4902	589	1159	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	82.0072	561	1159	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	81.596	529	1159	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	81.2645	552	1159	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	80.8327	479	1159	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 13:18:45,452] [INFO] GTDB search result was written to GCF_004208635.1_ASM420863v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:45,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:45,457] [INFO] DFAST_QC result json was written to GCF_004208635.1_ASM420863v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:45,457] [INFO] DFAST_QC completed!
[2024-01-24 13:18:45,457] [INFO] Total running time: 0h1m11s