[2024-01-25 20:18:05,929] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:05,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:05,932] [INFO] DQC Reference Directory: /var/lib/cwl/stga3bd4738-b848-4282-9394-2373a98df46d/dqc_reference
[2024-01-25 20:18:07,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:07,062] [INFO] Task started: Prodigal
[2024-01-25 20:18:07,062] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbd56dab-7f18-45d7-bdeb-8d55fdeb5b7d/GCF_900604955.1_PRJEB28794_genomic.fna.gz | prodigal -d GCF_900604955.1_PRJEB28794_genomic.fna/cds.fna -a GCF_900604955.1_PRJEB28794_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:12,582] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:12,583] [INFO] Task started: HMMsearch
[2024-01-25 20:18:12,583] [INFO] Running command: hmmsearch --tblout GCF_900604955.1_PRJEB28794_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3bd4738-b848-4282-9394-2373a98df46d/dqc_reference/reference_markers.hmm GCF_900604955.1_PRJEB28794_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:12,758] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:12,759] [INFO] Found 6/6 markers.
[2024-01-25 20:18:12,776] [INFO] Query marker FASTA was written to GCF_900604955.1_PRJEB28794_genomic.fna/markers.fasta
[2024-01-25 20:18:12,776] [INFO] Task started: Blastn
[2024-01-25 20:18:12,776] [INFO] Running command: blastn -query GCF_900604955.1_PRJEB28794_genomic.fna/markers.fasta -db /var/lib/cwl/stga3bd4738-b848-4282-9394-2373a98df46d/dqc_reference/reference_markers.fasta -out GCF_900604955.1_PRJEB28794_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:13,477] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:13,481] [INFO] Selected 28 target genomes.
[2024-01-25 20:18:13,481] [INFO] Target genome list was writen to GCF_900604955.1_PRJEB28794_genomic.fna/target_genomes.txt
[2024-01-25 20:18:13,510] [INFO] Task started: fastANI
[2024-01-25 20:18:13,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbd56dab-7f18-45d7-bdeb-8d55fdeb5b7d/GCF_900604955.1_PRJEB28794_genomic.fna.gz --refList GCF_900604955.1_PRJEB28794_genomic.fna/target_genomes.txt --output GCF_900604955.1_PRJEB28794_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:33,657] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:33,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3bd4738-b848-4282-9394-2373a98df46d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:33,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3bd4738-b848-4282-9394-2373a98df46d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:33,664] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:33,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:33,664] [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
Neoactinobaculum massilliense	strain=Marseille-P6182	GCA_900604955.1	2364794	2364794	type	True	100.0	620	622	95	conclusive
Actinotignum schaalii	strain=CCUG 27420	GCA_000724605.1	59505	59505	type	True	77.3014	76	622	95	below_threshold
Actinobaculum massiliense	strain=FC3	GCA_001457435.1	202789	202789	neotype	True	77.292	62	622	95	below_threshold
Actinotignum timonense	strain=type strain: Marseille-P2803	GCA_900155575.1	1870995	1870995	type	True	77.0386	82	622	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	76.909	51	622	95	below_threshold
Actinotignum schaalii	strain=DSM 15541	GCA_000429205.1	59505	59505	type	True	76.2618	74	622	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	75.6738	51	622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:33,665] [INFO] DFAST Taxonomy check result was written to GCF_900604955.1_PRJEB28794_genomic.fna/tc_result.tsv
[2024-01-25 20:18:33,666] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:33,666] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:33,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3bd4738-b848-4282-9394-2373a98df46d/dqc_reference/checkm_data
[2024-01-25 20:18:33,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:33,688] [INFO] Task started: CheckM
[2024-01-25 20:18:33,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900604955.1_PRJEB28794_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900604955.1_PRJEB28794_genomic.fna/checkm_input GCF_900604955.1_PRJEB28794_genomic.fna/checkm_result
[2024-01-25 20:18:54,286] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:54,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:54,304] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:54,304] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:54,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900604955.1_PRJEB28794_genomic.fna/markers.fasta)
[2024-01-25 20:18:54,304] [INFO] Task started: Blastn
[2024-01-25 20:18:54,305] [INFO] Running command: blastn -query GCF_900604955.1_PRJEB28794_genomic.fna/markers.fasta -db /var/lib/cwl/stga3bd4738-b848-4282-9394-2373a98df46d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900604955.1_PRJEB28794_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:55,332] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:55,335] [INFO] Selected 24 target genomes.
[2024-01-25 20:18:55,336] [INFO] Target genome list was writen to GCF_900604955.1_PRJEB28794_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:55,352] [INFO] Task started: fastANI
[2024-01-25 20:18:55,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbd56dab-7f18-45d7-bdeb-8d55fdeb5b7d/GCF_900604955.1_PRJEB28794_genomic.fna.gz --refList GCF_900604955.1_PRJEB28794_genomic.fna/target_genomes_gtdb.txt --output GCF_900604955.1_PRJEB28794_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:08,726] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:08,735] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:08,735] [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_900604955.1	s__Neoactinobaculum massilliense	100.0	620	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Neoactinobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006715165.1	s__Pseudarthrobacter sp006715165	77.6439	50	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000724605.1	s__Actinotignum schaalii	77.5009	77	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001457435.1	s__Actinobaculum massiliense	77.2447	62	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinobaculum	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900155575.1	s__Actinotignum timonense	77.1613	83	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	99.14	98.55	0.97	0.96	4	-
GCF_014137995.1	s__Promicromonospora sukumoe	77.0832	51	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411135.1	s__Actinotignum schaalii_A	76.8145	66	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:08,737] [INFO] GTDB search result was written to GCF_900604955.1_PRJEB28794_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:08,737] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:08,739] [INFO] DFAST_QC result json was written to GCF_900604955.1_PRJEB28794_genomic.fna/dqc_result.json
[2024-01-25 20:19:08,739] [INFO] DFAST_QC completed!
[2024-01-25 20:19:08,739] [INFO] Total running time: 0h1m3s