[2024-01-24 13:45:56,981] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:56,983] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:56,983] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5841823-a836-4d95-9794-2241462db746/dqc_reference
[2024-01-24 13:45:58,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:58,180] [INFO] Task started: Prodigal
[2024-01-24 13:45:58,180] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe5e0690-6007-4b19-b906-37e046384e33/GCF_022919155.1_ASM2291915v1_genomic.fna.gz | prodigal -d GCF_022919155.1_ASM2291915v1_genomic.fna/cds.fna -a GCF_022919155.1_ASM2291915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:07,597] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:07,597] [INFO] Task started: HMMsearch
[2024-01-24 13:46:07,597] [INFO] Running command: hmmsearch --tblout GCF_022919155.1_ASM2291915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5841823-a836-4d95-9794-2241462db746/dqc_reference/reference_markers.hmm GCF_022919155.1_ASM2291915v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:07,884] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:07,885] [INFO] Found 6/6 markers.
[2024-01-24 13:46:07,917] [INFO] Query marker FASTA was written to GCF_022919155.1_ASM2291915v1_genomic.fna/markers.fasta
[2024-01-24 13:46:07,918] [INFO] Task started: Blastn
[2024-01-24 13:46:07,918] [INFO] Running command: blastn -query GCF_022919155.1_ASM2291915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5841823-a836-4d95-9794-2241462db746/dqc_reference/reference_markers.fasta -out GCF_022919155.1_ASM2291915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:09,171] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:09,174] [INFO] Selected 20 target genomes.
[2024-01-24 13:46:09,175] [INFO] Target genome list was writen to GCF_022919155.1_ASM2291915v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:09,242] [INFO] Task started: fastANI
[2024-01-24 13:46:09,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe5e0690-6007-4b19-b906-37e046384e33/GCF_022919155.1_ASM2291915v1_genomic.fna.gz --refList GCF_022919155.1_ASM2291915v1_genomic.fna/target_genomes.txt --output GCF_022919155.1_ASM2291915v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:23,795] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:23,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5841823-a836-4d95-9794-2241462db746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:23,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5841823-a836-4d95-9794-2241462db746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:23,812] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:23,812] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:23,812] [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 muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	82.1389	641	1187	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	82.1028	602	1187	95	below_threshold
Leucobacter chromiiresistens	strain=JG 31	GCA_000231305.1	1079994	1079994	type	True	82.0785	596	1187	95	below_threshold
Leucobacter chromiiresistens	strain=DSM 22788	GCA_900102345.1	1079994	1079994	type	True	82.0207	627	1187	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	82.0141	676	1187	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	81.9588	621	1187	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	81.8327	586	1187	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	81.7918	633	1187	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	81.7674	555	1187	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	81.237	552	1187	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	80.3902	470	1187	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.1785	366	1187	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.8719	432	1187	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	77.8532	390	1187	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	77.5343	357	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:23,814] [INFO] DFAST Taxonomy check result was written to GCF_022919155.1_ASM2291915v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:23,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:23,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:23,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5841823-a836-4d95-9794-2241462db746/dqc_reference/checkm_data
[2024-01-24 13:46:23,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:23,851] [INFO] Task started: CheckM
[2024-01-24 13:46:23,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022919155.1_ASM2291915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022919155.1_ASM2291915v1_genomic.fna/checkm_input GCF_022919155.1_ASM2291915v1_genomic.fna/checkm_result
[2024-01-24 13:47:14,172] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:14,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:14,192] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:14,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:14,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022919155.1_ASM2291915v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:14,193] [INFO] Task started: Blastn
[2024-01-24 13:47:14,193] [INFO] Running command: blastn -query GCF_022919155.1_ASM2291915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5841823-a836-4d95-9794-2241462db746/dqc_reference/reference_markers_gtdb.fasta -out GCF_022919155.1_ASM2291915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:16,114] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:16,118] [INFO] Selected 19 target genomes.
[2024-01-24 13:47:16,119] [INFO] Target genome list was writen to GCF_022919155.1_ASM2291915v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:16,135] [INFO] Task started: fastANI
[2024-01-24 13:47:16,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe5e0690-6007-4b19-b906-37e046384e33/GCF_022919155.1_ASM2291915v1_genomic.fna.gz --refList GCF_022919155.1_ASM2291915v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022919155.1_ASM2291915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:31,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:31,280] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:31,280] [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_000421845.1	s__Leucobacter chironomi	82.1503	597	1187	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	82.1451	643	1187	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	81.9727	680	1187	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	81.8354	588	1187	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	81.8246	626	1187	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	81.7946	633	1187	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	81.7197	559	1187	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	81.6439	613	1187	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	81.2941	515	1187	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	81.2861	586	1187	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	80.807	551	1187	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	80.8034	530	1187	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	80.6763	565	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	99.99	99.99	0.99	0.98	9	-
GCA_002336855.1	s__Leucobacter sp002336855	78.6224	328	1187	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 13:47:31,282] [INFO] GTDB search result was written to GCF_022919155.1_ASM2291915v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:31,283] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:31,287] [INFO] DFAST_QC result json was written to GCF_022919155.1_ASM2291915v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:31,287] [INFO] DFAST_QC completed!
[2024-01-24 13:47:31,287] [INFO] Total running time: 0h1m34s