[2024-01-24 12:40:35,706] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:35,708] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:35,708] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe07af38-1744-4332-bf63-6c1b2b8b9aa3/dqc_reference
[2024-01-24 12:40:36,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:36,951] [INFO] Task started: Prodigal
[2024-01-24 12:40:36,951] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4ca08f7-fd1f-4214-a253-c7cd0df68d84/GCF_000425685.1_ASM42568v1_genomic.fna.gz | prodigal -d GCF_000425685.1_ASM42568v1_genomic.fna/cds.fna -a GCF_000425685.1_ASM42568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:46,892] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:46,893] [INFO] Task started: HMMsearch
[2024-01-24 12:40:46,893] [INFO] Running command: hmmsearch --tblout GCF_000425685.1_ASM42568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe07af38-1744-4332-bf63-6c1b2b8b9aa3/dqc_reference/reference_markers.hmm GCF_000425685.1_ASM42568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:47,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:47,134] [INFO] Found 6/6 markers.
[2024-01-24 12:40:47,165] [INFO] Query marker FASTA was written to GCF_000425685.1_ASM42568v1_genomic.fna/markers.fasta
[2024-01-24 12:40:47,165] [INFO] Task started: Blastn
[2024-01-24 12:40:47,166] [INFO] Running command: blastn -query GCF_000425685.1_ASM42568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe07af38-1744-4332-bf63-6c1b2b8b9aa3/dqc_reference/reference_markers.fasta -out GCF_000425685.1_ASM42568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:48,168] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:48,172] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:48,173] [INFO] Target genome list was writen to GCF_000425685.1_ASM42568v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:48,180] [INFO] Task started: fastANI
[2024-01-24 12:40:48,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ca08f7-fd1f-4214-a253-c7cd0df68d84/GCF_000425685.1_ASM42568v1_genomic.fna.gz --refList GCF_000425685.1_ASM42568v1_genomic.fna/target_genomes.txt --output GCF_000425685.1_ASM42568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:56,628] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:56,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe07af38-1744-4332-bf63-6c1b2b8b9aa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:56,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe07af38-1744-4332-bf63-6c1b2b8b9aa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:56,642] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:56,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:56,643] [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
Gulosibacter molinativorax	strain=DSM 13485	GCA_000425685.1	256821	256821	type	True	100.0	1086	1088	95	conclusive
Gulosibacter molinativorax	strain=ON4	GCA_003010915.2	256821	256821	type	True	99.9911	1087	1088	95	conclusive
Gulosibacter chungangensis	strain=KCTC 13959	GCA_008831155.1	979746	979746	type	True	81.1512	520	1088	95	below_threshold
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	79.5782	397	1088	95	below_threshold
Gulosibacter macacae	strain=YIM 102482-1	GCA_003865375.1	2488791	2488791	type	True	78.8126	301	1088	95	below_threshold
Gulosibacter bifidus	strain=NBRC 103089	GCA_001570925.1	272239	272239	type	True	78.4615	192	1088	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.3801	235	1088	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.3708	188	1088	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	77.3538	184	1088	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	77.2823	236	1088	95	below_threshold
Agromyces intestinalis	strain=KACC 19306	GCA_008365295.1	2592652	2592652	type	True	77.2031	212	1088	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	76.9992	196	1088	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	76.303	143	1088	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.2918	149	1088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:56,644] [INFO] DFAST Taxonomy check result was written to GCF_000425685.1_ASM42568v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:56,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:56,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:56,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe07af38-1744-4332-bf63-6c1b2b8b9aa3/dqc_reference/checkm_data
[2024-01-24 12:40:56,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:56,684] [INFO] Task started: CheckM
[2024-01-24 12:40:56,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425685.1_ASM42568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425685.1_ASM42568v1_genomic.fna/checkm_input GCF_000425685.1_ASM42568v1_genomic.fna/checkm_result
[2024-01-24 12:41:29,231] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:29,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:29,252] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:29,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:29,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425685.1_ASM42568v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:29,253] [INFO] Task started: Blastn
[2024-01-24 12:41:29,253] [INFO] Running command: blastn -query GCF_000425685.1_ASM42568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe07af38-1744-4332-bf63-6c1b2b8b9aa3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425685.1_ASM42568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:30,708] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:30,712] [INFO] Selected 13 target genomes.
[2024-01-24 12:41:30,713] [INFO] Target genome list was writen to GCF_000425685.1_ASM42568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:30,726] [INFO] Task started: fastANI
[2024-01-24 12:41:30,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ca08f7-fd1f-4214-a253-c7cd0df68d84/GCF_000425685.1_ASM42568v1_genomic.fna.gz --refList GCF_000425685.1_ASM42568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425685.1_ASM42568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:38,768] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:38,781] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:38,782] [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_000425685.1	s__Gulosibacter molinativorax	100.0	1086	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_008831155.1	s__Gulosibacter chungangensis	81.1512	520	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163695.1	s__Gulosibacter sp900163695	80.1849	455	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626105.1	s__Gulosibacter sp900626105	79.7103	390	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	98.80	98.80	0.92	0.92	2	-
GCF_000381765.1	s__Gulosibacter faecalis	79.584	397	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719255.1	s__Gulosibacter sp012719255	79.2247	330	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002931055.1	s__Pseudoclavibacter sp002931055	77.7483	234	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	97.65	95.42	0.90	0.86	11	-
GCF_018308945.1	s__Agrococcus sp018308945	77.4614	258	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135055.1	s__Agromyces binzhouensis	77.3134	175	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907355.1	s__Agromyces aurantiacus	77.2589	238	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674665.1	s__Agromyces kandeliae	77.1603	215	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634985.1	s__Agromyces sp003634985	77.0262	216	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538725.1	s__Cellulomonas gelida	76.566	140	1088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.61	99.23	0.96	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:38,783] [INFO] GTDB search result was written to GCF_000425685.1_ASM42568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:38,784] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:38,787] [INFO] DFAST_QC result json was written to GCF_000425685.1_ASM42568v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:38,787] [INFO] DFAST_QC completed!
[2024-01-24 12:41:38,787] [INFO] Total running time: 0h1m3s