[2024-01-24 13:41:40,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a85bf3c-a14d-4de7-875b-f8d9f6c65bcc/dqc_reference
[2024-01-24 13:41:42,003] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,004] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,005] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2e48a92-44cb-4204-8894-5a35b81f6164/GCF_004078655.1_ASM407865v1_genomic.fna.gz | prodigal -d GCF_004078655.1_ASM407865v1_genomic.fna/cds.fna -a GCF_004078655.1_ASM407865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:51,744] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:51,745] [INFO] Task started: HMMsearch
[2024-01-24 13:41:51,745] [INFO] Running command: hmmsearch --tblout GCF_004078655.1_ASM407865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a85bf3c-a14d-4de7-875b-f8d9f6c65bcc/dqc_reference/reference_markers.hmm GCF_004078655.1_ASM407865v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:52,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:52,023] [INFO] Found 6/6 markers.
[2024-01-24 13:41:52,057] [INFO] Query marker FASTA was written to GCF_004078655.1_ASM407865v1_genomic.fna/markers.fasta
[2024-01-24 13:41:52,058] [INFO] Task started: Blastn
[2024-01-24 13:41:52,058] [INFO] Running command: blastn -query GCF_004078655.1_ASM407865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a85bf3c-a14d-4de7-875b-f8d9f6c65bcc/dqc_reference/reference_markers.fasta -out GCF_004078655.1_ASM407865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:53,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:53,291] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:53,291] [INFO] Target genome list was writen to GCF_004078655.1_ASM407865v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:53,295] [INFO] Task started: fastANI
[2024-01-24 13:41:53,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e48a92-44cb-4204-8894-5a35b81f6164/GCF_004078655.1_ASM407865v1_genomic.fna.gz --refList GCF_004078655.1_ASM407865v1_genomic.fna/target_genomes.txt --output GCF_004078655.1_ASM407865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:02,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:02,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a85bf3c-a14d-4de7-875b-f8d9f6c65bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:02,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a85bf3c-a14d-4de7-875b-f8d9f6c65bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:02,905] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:02,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:02,906] [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
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	100.0	1131	1132	95	conclusive
Labedella phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	86.8027	928	1132	95	below_threshold
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	82.7144	763	1132	95	below_threshold
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	82.6481	796	1132	95	below_threshold
Labedella gwakjiensis	strain=DSM 21548	GCA_003014675.1	390269	390269	type	True	82.6408	764	1132	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.9111	392	1132	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.7738	392	1132	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.6996	373	1132	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.6645	386	1132	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.5045	374	1132	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.4234	379	1132	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.2793	381	1132	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	78.0308	349	1132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:02,907] [INFO] DFAST Taxonomy check result was written to GCF_004078655.1_ASM407865v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:02,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:02,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:02,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a85bf3c-a14d-4de7-875b-f8d9f6c65bcc/dqc_reference/checkm_data
[2024-01-24 13:42:02,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:02,951] [INFO] Task started: CheckM
[2024-01-24 13:42:02,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004078655.1_ASM407865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004078655.1_ASM407865v1_genomic.fna/checkm_input GCF_004078655.1_ASM407865v1_genomic.fna/checkm_result
[2024-01-24 13:42:49,271] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:49,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:49,296] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:49,297] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:49,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004078655.1_ASM407865v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:49,298] [INFO] Task started: Blastn
[2024-01-24 13:42:49,298] [INFO] Running command: blastn -query GCF_004078655.1_ASM407865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a85bf3c-a14d-4de7-875b-f8d9f6c65bcc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004078655.1_ASM407865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:51,097] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:51,100] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:51,100] [INFO] Target genome list was writen to GCF_004078655.1_ASM407865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:51,127] [INFO] Task started: fastANI
[2024-01-24 13:42:51,127] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e48a92-44cb-4204-8894-5a35b81f6164/GCF_004078655.1_ASM407865v1_genomic.fna.gz --refList GCF_004078655.1_ASM407865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004078655.1_ASM407865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:00,999] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:01,022] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:01,022] [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_004078655.1	s__Labedella populi	100.0	1131	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004078635.1	s__Labedella phragmitis	86.7894	929	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014675.1	s__Labedella gwakjiensis	82.63	765	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003990045.1	s__Labedella endophytica	82.6207	799	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	78.8831	395	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	78.8363	406	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384855.1	s__Agromyces sp003384855	78.7196	417	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751785.1	s__Frigoribacterium sp003751785	78.6903	371	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789225.1	s__WSTA01 sp009789225	78.6169	392	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402485.1	s__Cryobacterium sp004402485	78.3402	327	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427145.1	s__Microbacterium sp001427145	78.1407	309	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	78.061	346	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	77.9708	360	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:01,024] [INFO] GTDB search result was written to GCF_004078655.1_ASM407865v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:01,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:01,028] [INFO] DFAST_QC result json was written to GCF_004078655.1_ASM407865v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:01,029] [INFO] DFAST_QC completed!
[2024-01-24 13:43:01,029] [INFO] Total running time: 0h1m20s