[2024-01-24 12:13:36,081] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:36,087] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:36,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg272c564c-9af4-4d8b-a3d6-93fd0744596b/dqc_reference
[2024-01-24 12:13:37,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:37,293] [INFO] Task started: Prodigal
[2024-01-24 12:13:37,294] [INFO] Running command: gunzip -c /var/lib/cwl/stg27ffa39d-e30b-4527-a38b-659c213eda9c/GCF_000024065.1_ASM2406v1_genomic.fna.gz | prodigal -d GCF_000024065.1_ASM2406v1_genomic.fna/cds.fna -a GCF_000024065.1_ASM2406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:47,229] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:47,229] [INFO] Task started: HMMsearch
[2024-01-24 12:13:47,229] [INFO] Running command: hmmsearch --tblout GCF_000024065.1_ASM2406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg272c564c-9af4-4d8b-a3d6-93fd0744596b/dqc_reference/reference_markers.hmm GCF_000024065.1_ASM2406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:47,526] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:47,527] [INFO] Found 6/6 markers.
[2024-01-24 12:13:47,567] [INFO] Query marker FASTA was written to GCF_000024065.1_ASM2406v1_genomic.fna/markers.fasta
[2024-01-24 12:13:47,567] [INFO] Task started: Blastn
[2024-01-24 12:13:47,567] [INFO] Running command: blastn -query GCF_000024065.1_ASM2406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg272c564c-9af4-4d8b-a3d6-93fd0744596b/dqc_reference/reference_markers.fasta -out GCF_000024065.1_ASM2406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:48,282] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:48,286] [INFO] Selected 13 target genomes.
[2024-01-24 12:13:48,287] [INFO] Target genome list was writen to GCF_000024065.1_ASM2406v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:48,317] [INFO] Task started: fastANI
[2024-01-24 12:13:48,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ffa39d-e30b-4527-a38b-659c213eda9c/GCF_000024065.1_ASM2406v1_genomic.fna.gz --refList GCF_000024065.1_ASM2406v1_genomic.fna/target_genomes.txt --output GCF_000024065.1_ASM2406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:55,996] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:55,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg272c564c-9af4-4d8b-a3d6-93fd0744596b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:55,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg272c564c-9af4-4d8b-a3d6-93fd0744596b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:56,004] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:13:56,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:56,005] [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
Jonesia denitrificans	strain=DSM 20603	GCA_000024065.1	43674	43674	type	True	100.0	915	916	95	conclusive
Jonesia denitrificans	strain=NCTC10816	GCA_900475835.1	43674	43674	type	True	99.9999	914	916	95	conclusive
Jonesia denitrificans	strain=FDAARGOS 1440	GCA_019048465.1	43674	43674	type	True	99.9996	915	916	95	conclusive
Jonesia quinghaiensis	strain=DSM 15701	GCA_000423205.1	262806	262806	type	True	78.7204	297	916	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	78.3062	67	916	95	below_threshold
Timonella senegalensis		GCA_000312125.1	1465825	1465825	type	True	77.786	95	916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:56,007] [INFO] DFAST Taxonomy check result was written to GCF_000024065.1_ASM2406v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:56,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:56,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:56,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg272c564c-9af4-4d8b-a3d6-93fd0744596b/dqc_reference/checkm_data
[2024-01-24 12:13:56,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:56,041] [INFO] Task started: CheckM
[2024-01-24 12:13:56,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024065.1_ASM2406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024065.1_ASM2406v1_genomic.fna/checkm_input GCF_000024065.1_ASM2406v1_genomic.fna/checkm_result
[2024-01-24 12:14:32,302] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:32,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:32,321] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:32,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:32,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024065.1_ASM2406v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:32,322] [INFO] Task started: Blastn
[2024-01-24 12:14:32,322] [INFO] Running command: blastn -query GCF_000024065.1_ASM2406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg272c564c-9af4-4d8b-a3d6-93fd0744596b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024065.1_ASM2406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:33,369] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:33,372] [INFO] Selected 27 target genomes.
[2024-01-24 12:14:33,372] [INFO] Target genome list was writen to GCF_000024065.1_ASM2406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:33,395] [INFO] Task started: fastANI
[2024-01-24 12:14:33,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ffa39d-e30b-4527-a38b-659c213eda9c/GCF_000024065.1_ASM2406v1_genomic.fna.gz --refList GCF_000024065.1_ASM2406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024065.1_ASM2406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:47,178] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:47,184] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:47,184] [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_000024065.1	s__Jonesia denitrificans	100.0	915	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Jonesia	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_000423205.1	s__Jonesia quinghaiensis	78.7204	297	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Jonesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	78.4609	55	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_000024925.1	s__Sanguibacter keddieii	78.3242	67	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312125.1	s__Timonella senegalensis	77.8303	95	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Timonella	95.0	98.10	97.43	0.93	0.89	5	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	76.9108	52	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:47,186] [INFO] GTDB search result was written to GCF_000024065.1_ASM2406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:47,187] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:47,189] [INFO] DFAST_QC result json was written to GCF_000024065.1_ASM2406v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:47,189] [INFO] DFAST_QC completed!
[2024-01-24 12:14:47,189] [INFO] Total running time: 0h1m11s