[2024-01-24 13:13:26,478] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:26,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:26,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg522b2bb2-8744-42ae-8e56-2a736b487581/dqc_reference
[2024-01-24 13:13:27,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:27,814] [INFO] Task started: Prodigal
[2024-01-24 13:13:27,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg41503655-1fc8-4648-8ddd-c376d84d91da/GCF_003399685.1_ASM339968v1_genomic.fna.gz | prodigal -d GCF_003399685.1_ASM339968v1_genomic.fna/cds.fna -a GCF_003399685.1_ASM339968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:40,621] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:40,621] [INFO] Task started: HMMsearch
[2024-01-24 13:13:40,621] [INFO] Running command: hmmsearch --tblout GCF_003399685.1_ASM339968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg522b2bb2-8744-42ae-8e56-2a736b487581/dqc_reference/reference_markers.hmm GCF_003399685.1_ASM339968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:40,936] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:40,937] [INFO] Found 6/6 markers.
[2024-01-24 13:13:40,978] [INFO] Query marker FASTA was written to GCF_003399685.1_ASM339968v1_genomic.fna/markers.fasta
[2024-01-24 13:13:40,979] [INFO] Task started: Blastn
[2024-01-24 13:13:40,979] [INFO] Running command: blastn -query GCF_003399685.1_ASM339968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg522b2bb2-8744-42ae-8e56-2a736b487581/dqc_reference/reference_markers.fasta -out GCF_003399685.1_ASM339968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:42,216] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:42,219] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:42,219] [INFO] Target genome list was writen to GCF_003399685.1_ASM339968v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:42,255] [INFO] Task started: fastANI
[2024-01-24 13:13:42,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg41503655-1fc8-4648-8ddd-c376d84d91da/GCF_003399685.1_ASM339968v1_genomic.fna.gz --refList GCF_003399685.1_ASM339968v1_genomic.fna/target_genomes.txt --output GCF_003399685.1_ASM339968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:54,702] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:54,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg522b2bb2-8744-42ae-8e56-2a736b487581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:54,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg522b2bb2-8744-42ae-8e56-2a736b487581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:54,722] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:54,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:54,722] [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
Subtercola boreus	strain=K300	GCA_003399685.1	120213	120213	suspected-type	True	100.0	1402	1404	95	conclusive
Subtercola boreus	strain=DSM 13056	GCA_006716115.1	120213	120213	suspected-type	True	99.9994	1402	1404	95	conclusive
Subtercola vilae	strain=DB165	GCA_004923255.1	2056433	2056433	type	True	80.9854	621	1404	95	below_threshold
Subtercola frigoramans	strain=DSM 13057	GCA_016907385.1	120298	120298	type	True	80.6013	566	1404	95	below_threshold
Subtercola lobariae	strain=9583b	GCA_016881145.1	1588641	1588641	type	True	80.1151	575	1404	95	below_threshold
Subtercola lobariae	strain=CGMCC 1.12976	GCA_014640255.1	1588641	1588641	type	True	80.0623	575	1404	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.9408	561	1404	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	79.7912	514	1404	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	79.3784	522	1404	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.5161	422	1404	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.4206	383	1404	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.4104	404	1404	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.3905	412	1404	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.2787	356	1404	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:54,724] [INFO] DFAST Taxonomy check result was written to GCF_003399685.1_ASM339968v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:54,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:54,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:54,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg522b2bb2-8744-42ae-8e56-2a736b487581/dqc_reference/checkm_data
[2024-01-24 13:13:54,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:54,771] [INFO] Task started: CheckM
[2024-01-24 13:13:54,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003399685.1_ASM339968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003399685.1_ASM339968v1_genomic.fna/checkm_input GCF_003399685.1_ASM339968v1_genomic.fna/checkm_result
[2024-01-24 13:15:00,472] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:00,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:00,498] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:00,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:00,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003399685.1_ASM339968v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:00,499] [INFO] Task started: Blastn
[2024-01-24 13:15:00,499] [INFO] Running command: blastn -query GCF_003399685.1_ASM339968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg522b2bb2-8744-42ae-8e56-2a736b487581/dqc_reference/reference_markers_gtdb.fasta -out GCF_003399685.1_ASM339968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:02,314] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:02,318] [INFO] Selected 6 target genomes.
[2024-01-24 13:15:02,318] [INFO] Target genome list was writen to GCF_003399685.1_ASM339968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:02,333] [INFO] Task started: fastANI
[2024-01-24 13:15:02,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg41503655-1fc8-4648-8ddd-c376d84d91da/GCF_003399685.1_ASM339968v1_genomic.fna.gz --refList GCF_003399685.1_ASM339968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003399685.1_ASM339968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:08,075] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:08,086] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:08,087] [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_006716115.1	s__Subtercola boreus	99.9994	1401	1404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003399635.1	s__Subtercola boreus_B	86.9341	941	1404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399625.1	s__Subtercola boreus_C	86.6993	963	1404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002931235.1	s__Subtercola sp002931235	84.5804	787	1404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399645.1	s__Subtercola boreus_A	83.3778	835	1404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	100.00	100.00	0.99	0.99	3	-
GCF_018889995.1	s__Subtercola sp018889995	80.4161	565	1404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:08,088] [INFO] GTDB search result was written to GCF_003399685.1_ASM339968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:08,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:08,092] [INFO] DFAST_QC result json was written to GCF_003399685.1_ASM339968v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:08,092] [INFO] DFAST_QC completed!
[2024-01-24 13:15:08,092] [INFO] Total running time: 0h1m42s