[2023-06-13 04:23:30,353] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:23:30,359] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:23:30,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgf21f5424-8da5-4c18-be83-5aa0475bfa38/dqc_reference
[2023-06-13 04:23:31,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:23:31,629] [INFO] Task started: Prodigal
[2023-06-13 04:23:31,630] [INFO] Running command: gunzip -c /var/lib/cwl/stgef4903b3-67cd-47db-a2bc-2b232d176b4f/GCA_022360155.1_ASM2236015v1_genomic.fna.gz | prodigal -d GCA_022360155.1_ASM2236015v1_genomic.fna/cds.fna -a GCA_022360155.1_ASM2236015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:23:53,618] [INFO] Task succeeded: Prodigal
[2023-06-13 04:23:53,619] [INFO] Task started: HMMsearch
[2023-06-13 04:23:53,619] [INFO] Running command: hmmsearch --tblout GCA_022360155.1_ASM2236015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf21f5424-8da5-4c18-be83-5aa0475bfa38/dqc_reference/reference_markers.hmm GCA_022360155.1_ASM2236015v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:23:53,978] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:23:53,980] [INFO] Found 6/6 markers.
[2023-06-13 04:23:54,045] [INFO] Query marker FASTA was written to GCA_022360155.1_ASM2236015v1_genomic.fna/markers.fasta
[2023-06-13 04:23:54,046] [INFO] Task started: Blastn
[2023-06-13 04:23:54,046] [INFO] Running command: blastn -query GCA_022360155.1_ASM2236015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf21f5424-8da5-4c18-be83-5aa0475bfa38/dqc_reference/reference_markers.fasta -out GCA_022360155.1_ASM2236015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:23:54,611] [INFO] Task succeeded: Blastn
[2023-06-13 04:23:54,619] [INFO] Selected 20 target genomes.
[2023-06-13 04:23:54,620] [INFO] Target genome list was writen to GCA_022360155.1_ASM2236015v1_genomic.fna/target_genomes.txt
[2023-06-13 04:23:54,624] [INFO] Task started: fastANI
[2023-06-13 04:23:54,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgef4903b3-67cd-47db-a2bc-2b232d176b4f/GCA_022360155.1_ASM2236015v1_genomic.fna.gz --refList GCA_022360155.1_ASM2236015v1_genomic.fna/target_genomes.txt --output GCA_022360155.1_ASM2236015v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:24:07,182] [INFO] Task succeeded: fastANI
[2023-06-13 04:24:07,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf21f5424-8da5-4c18-be83-5aa0475bfa38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:24:07,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf21f5424-8da5-4c18-be83-5aa0475bfa38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:24:07,190] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:24:07,190] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 04:24:07,190] [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
Roseiflexus castenholzii	strain=DSM 13941	GCA_000017805.1	120962	120962	type	True	75.543	70	2454	95	below_threshold
Oscillochloris trichoides	strain=DG-6	GCA_000152145.1	104176	104176	type	True	75.4688	71	2454	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 04:24:07,192] [INFO] DFAST Taxonomy check result was written to GCA_022360155.1_ASM2236015v1_genomic.fna/tc_result.tsv
[2023-06-13 04:24:07,193] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:24:07,193] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:24:07,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf21f5424-8da5-4c18-be83-5aa0475bfa38/dqc_reference/checkm_data
[2023-06-13 04:24:07,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:24:07,278] [INFO] Task started: CheckM
[2023-06-13 04:24:07,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022360155.1_ASM2236015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022360155.1_ASM2236015v1_genomic.fna/checkm_input GCA_022360155.1_ASM2236015v1_genomic.fna/checkm_result
[2023-06-13 04:25:11,794] [INFO] Task succeeded: CheckM
[2023-06-13 04:25:11,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.41%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:25:11,825] [INFO] ===== Completeness check finished =====
[2023-06-13 04:25:11,826] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:25:11,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022360155.1_ASM2236015v1_genomic.fna/markers.fasta)
[2023-06-13 04:25:11,827] [INFO] Task started: Blastn
[2023-06-13 04:25:11,827] [INFO] Running command: blastn -query GCA_022360155.1_ASM2236015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf21f5424-8da5-4c18-be83-5aa0475bfa38/dqc_reference/reference_markers_gtdb.fasta -out GCA_022360155.1_ASM2236015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:25:12,539] [INFO] Task succeeded: Blastn
[2023-06-13 04:25:12,545] [INFO] Selected 24 target genomes.
[2023-06-13 04:25:12,545] [INFO] Target genome list was writen to GCA_022360155.1_ASM2236015v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:25:12,564] [INFO] Task started: fastANI
[2023-06-13 04:25:12,564] [INFO] Running command: fastANI --query /var/lib/cwl/stgef4903b3-67cd-47db-a2bc-2b232d176b4f/GCA_022360155.1_ASM2236015v1_genomic.fna.gz --refList GCA_022360155.1_ASM2236015v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022360155.1_ASM2236015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:25:28,411] [INFO] Task succeeded: fastANI
[2023-06-13 04:25:28,423] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 04:25:28,423] [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
GCA_012033195.1	s__JAAUSQ01 sp012033195	75.6749	57	2454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JAAUSQ01	95.0	99.36	99.36	0.84	0.84	2	-
GCF_004138135.1	s__Oscillochloris fontis	75.6164	63	2454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017805.1	s__Roseiflexus castenholzii	75.543	70	2454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Roseiflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152145.1	s__Oscillochloris trichoides	75.4688	71	2454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032775.1	s__JAAUQO01 sp012032775	75.4417	79	2454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JAAUQO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717335.1	s__JADKFS01 sp016717335	75.3973	153	2454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JADKFS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887465.1	s__Oscillochloris sp903887465	75.208	97	2454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	99.82	99.74	0.95	0.93	6	-
GCA_903916565.1	s__CAIWXH01 sp903916565	75.1366	84	2454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__CAIWXH01	95.0	98.56	98.56	0.77	0.77	2	-
GCA_013538855.1	s__OHK22 sp013538855	74.7585	64	2454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__OHK22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 04:25:28,440] [INFO] GTDB search result was written to GCA_022360155.1_ASM2236015v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:25:28,441] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:25:28,445] [INFO] DFAST_QC result json was written to GCA_022360155.1_ASM2236015v1_genomic.fna/dqc_result.json
[2023-06-13 04:25:28,446] [INFO] DFAST_QC completed!
[2023-06-13 04:25:28,446] [INFO] Total running time: 0h1m58s