[2024-01-24 12:31:58,730] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,733] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,733] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcaa3f45-4f6b-4722-9e00-d25c252f3839/dqc_reference
[2024-01-24 12:32:00,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:32:00,127] [INFO] Task started: Prodigal
[2024-01-24 12:32:00,127] [INFO] Running command: gunzip -c /var/lib/cwl/stgc297b361-723d-4afb-82b2-8f4d081bde51/GCF_000526375.1_ASM52637v1_genomic.fna.gz | prodigal -d GCF_000526375.1_ASM52637v1_genomic.fna/cds.fna -a GCF_000526375.1_ASM52637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:10,081] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:10,082] [INFO] Task started: HMMsearch
[2024-01-24 12:32:10,082] [INFO] Running command: hmmsearch --tblout GCF_000526375.1_ASM52637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcaa3f45-4f6b-4722-9e00-d25c252f3839/dqc_reference/reference_markers.hmm GCF_000526375.1_ASM52637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:10,350] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:10,351] [INFO] Found 6/6 markers.
[2024-01-24 12:32:10,388] [INFO] Query marker FASTA was written to GCF_000526375.1_ASM52637v1_genomic.fna/markers.fasta
[2024-01-24 12:32:10,389] [INFO] Task started: Blastn
[2024-01-24 12:32:10,389] [INFO] Running command: blastn -query GCF_000526375.1_ASM52637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcaa3f45-4f6b-4722-9e00-d25c252f3839/dqc_reference/reference_markers.fasta -out GCF_000526375.1_ASM52637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:11,001] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:11,007] [INFO] Selected 18 target genomes.
[2024-01-24 12:32:11,007] [INFO] Target genome list was writen to GCF_000526375.1_ASM52637v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:11,013] [INFO] Task started: fastANI
[2024-01-24 12:32:11,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgc297b361-723d-4afb-82b2-8f4d081bde51/GCF_000526375.1_ASM52637v1_genomic.fna.gz --refList GCF_000526375.1_ASM52637v1_genomic.fna/target_genomes.txt --output GCF_000526375.1_ASM52637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:27,036] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:27,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcaa3f45-4f6b-4722-9e00-d25c252f3839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:27,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcaa3f45-4f6b-4722-9e00-d25c252f3839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:27,041] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:27,042] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:27,042] [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
Aminiphilus circumscriptus	strain=DSM 16581	GCA_000526375.1	290732	290732	type	True	100.0	1071	1072	95	conclusive
Aminomonas paucivorans	strain=DSM 12260	GCA_000165795.1	81412	81412	type	True	77.2575	111	1072	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:27,043] [INFO] DFAST Taxonomy check result was written to GCF_000526375.1_ASM52637v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:27,044] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:27,044] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:27,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcaa3f45-4f6b-4722-9e00-d25c252f3839/dqc_reference/checkm_data
[2024-01-24 12:32:27,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:27,084] [INFO] Task started: CheckM
[2024-01-24 12:32:27,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000526375.1_ASM52637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000526375.1_ASM52637v1_genomic.fna/checkm_input GCF_000526375.1_ASM52637v1_genomic.fna/checkm_result
[2024-01-24 12:33:01,175] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:01,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:01,197] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:01,198] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:01,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000526375.1_ASM52637v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:01,199] [INFO] Task started: Blastn
[2024-01-24 12:33:01,199] [INFO] Running command: blastn -query GCF_000526375.1_ASM52637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcaa3f45-4f6b-4722-9e00-d25c252f3839/dqc_reference/reference_markers_gtdb.fasta -out GCF_000526375.1_ASM52637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:02,011] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:02,015] [INFO] Selected 16 target genomes.
[2024-01-24 12:33:02,015] [INFO] Target genome list was writen to GCF_000526375.1_ASM52637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:02,050] [INFO] Task started: fastANI
[2024-01-24 12:33:02,051] [INFO] Running command: fastANI --query /var/lib/cwl/stgc297b361-723d-4afb-82b2-8f4d081bde51/GCF_000526375.1_ASM52637v1_genomic.fna.gz --refList GCF_000526375.1_ASM52637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000526375.1_ASM52637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:10,317] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:10,332] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:10,332] [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_000526375.1	s__Aminiphilus circumscriptus	100.0	1071	1072	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminiphilaceae;g__Aminiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002425685.1	s__Aminiphilus sp002425685	93.4322	764	1072	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminiphilaceae;g__Aminiphilus	95.0	98.97	98.23	0.86	0.86	3	-
GCA_018398915.1	s__SV1-B22 sp018398915	77.972	105	1072	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__SV1-B22;g__SV1-B22	95.0	99.20	99.20	0.94	0.94	2	-
GCF_000165795.1	s__Aminomonas paucivorans	77.3992	111	1072	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Aminomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016756725.1	s__SV1-B22 sp016756725	76.7992	90	1072	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__SV1-B22;g__SV1-B22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018433595.1	s__SV1-B22 sp018433595	76.6178	77	1072	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__SV1-B22;g__SV1-B22	95.0	98.92	97.17	0.90	0.86	7	-
GCA_016756745.1	s__Aminivibrio sp016756745	76.1146	66	1072	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:10,334] [INFO] GTDB search result was written to GCF_000526375.1_ASM52637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:10,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:10,338] [INFO] DFAST_QC result json was written to GCF_000526375.1_ASM52637v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:10,339] [INFO] DFAST_QC completed!
[2024-01-24 12:33:10,339] [INFO] Total running time: 0h1m12s