[2024-01-24 10:47:54,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,164] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,165] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf08a616-16bf-4d31-b844-f1f0e74d312f/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,343] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,343] [INFO] Running command: gunzip -c /var/lib/cwl/stg99786e45-c62d-4756-9d60-44e2b2200e76/GCF_019048465.1_ASM1904846v1_genomic.fna.gz | prodigal -d GCF_019048465.1_ASM1904846v1_genomic.fna/cds.fna -a GCF_019048465.1_ASM1904846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:13,116] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:13,116] [INFO] Task started: HMMsearch
[2024-01-24 10:48:13,116] [INFO] Running command: hmmsearch --tblout GCF_019048465.1_ASM1904846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf08a616-16bf-4d31-b844-f1f0e74d312f/dqc_reference/reference_markers.hmm GCF_019048465.1_ASM1904846v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:13,366] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:13,368] [INFO] Found 6/6 markers.
[2024-01-24 10:48:13,399] [INFO] Query marker FASTA was written to GCF_019048465.1_ASM1904846v1_genomic.fna/markers.fasta
[2024-01-24 10:48:13,399] [INFO] Task started: Blastn
[2024-01-24 10:48:13,399] [INFO] Running command: blastn -query GCF_019048465.1_ASM1904846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf08a616-16bf-4d31-b844-f1f0e74d312f/dqc_reference/reference_markers.fasta -out GCF_019048465.1_ASM1904846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:14,079] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:14,084] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:14,085] [INFO] Target genome list was writen to GCF_019048465.1_ASM1904846v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:14,092] [INFO] Task started: fastANI
[2024-01-24 10:48:14,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg99786e45-c62d-4756-9d60-44e2b2200e76/GCF_019048465.1_ASM1904846v1_genomic.fna.gz --refList GCF_019048465.1_ASM1904846v1_genomic.fna/target_genomes.txt --output GCF_019048465.1_ASM1904846v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:21,735] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:21,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf08a616-16bf-4d31-b844-f1f0e74d312f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:21,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf08a616-16bf-4d31-b844-f1f0e74d312f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:21,744] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:48:21,745] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:21,745] [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=FDAARGOS 1440	GCA_019048465.1	43674	43674	type	True	100.0	915	916	95	conclusive
Jonesia denitrificans	strain=NCTC10816	GCA_900475835.1	43674	43674	type	True	99.9999	915	916	95	conclusive
Jonesia denitrificans	strain=DSM 20603	GCA_000024065.1	43674	43674	type	True	99.9997	915	916	95	conclusive
Jonesia quinghaiensis	strain=DSM 15701	GCA_000423205.1	262806	262806	type	True	78.8039	303	916	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	78.5865	68	916	95	below_threshold
Timonella senegalensis		GCA_000312125.1	1465825	1465825	type	True	78.039	92	916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:21,746] [INFO] DFAST Taxonomy check result was written to GCF_019048465.1_ASM1904846v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:21,747] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:21,747] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:21,747] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf08a616-16bf-4d31-b844-f1f0e74d312f/dqc_reference/checkm_data
[2024-01-24 10:48:21,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:21,778] [INFO] Task started: CheckM
[2024-01-24 10:48:21,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019048465.1_ASM1904846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019048465.1_ASM1904846v1_genomic.fna/checkm_input GCF_019048465.1_ASM1904846v1_genomic.fna/checkm_result
[2024-01-24 10:48:57,254] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:57,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:57,277] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:57,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:57,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019048465.1_ASM1904846v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:57,278] [INFO] Task started: Blastn
[2024-01-24 10:48:57,278] [INFO] Running command: blastn -query GCF_019048465.1_ASM1904846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf08a616-16bf-4d31-b844-f1f0e74d312f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019048465.1_ASM1904846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:58,264] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:58,269] [INFO] Selected 27 target genomes.
[2024-01-24 10:48:58,269] [INFO] Target genome list was writen to GCF_019048465.1_ASM1904846v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:58,290] [INFO] Task started: fastANI
[2024-01-24 10:48:58,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg99786e45-c62d-4756-9d60-44e2b2200e76/GCF_019048465.1_ASM1904846v1_genomic.fna.gz --refList GCF_019048465.1_ASM1904846v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019048465.1_ASM1904846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:12,292] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:12,303] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:12,303] [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	99.9997	916	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	78.8101	302	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_000024925.1	s__Sanguibacter keddieii	78.7673	69	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_016907755.1	s__Cellulosimicrobium cellulans_D	78.3389	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_000215105.1	s__Isoptericola variabilis_A	78.1482	53	916	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_000312125.1	s__Timonella senegalensis	78.0463	93	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	77.0515	50	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 10:49:12,305] [INFO] GTDB search result was written to GCF_019048465.1_ASM1904846v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:12,306] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:12,308] [INFO] DFAST_QC result json was written to GCF_019048465.1_ASM1904846v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:12,309] [INFO] DFAST_QC completed!
[2024-01-24 10:49:12,309] [INFO] Total running time: 0h1m18s