[2023-06-27 10:11:38,778] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:11:38,792] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:11:38,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b77be32-3540-4767-9b5b-1d519eb54bee/dqc_reference
[2023-06-27 10:11:40,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:11:40,799] [INFO] Task started: Prodigal
[2023-06-27 10:11:40,799] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bbf7908-7519-442e-b39d-004c4fe141fa/GCA_026706455.1_ASM2670645v1_genomic.fna.gz | prodigal -d GCA_026706455.1_ASM2670645v1_genomic.fna/cds.fna -a GCA_026706455.1_ASM2670645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:11:51,140] [INFO] Task succeeded: Prodigal
[2023-06-27 10:11:51,141] [INFO] Task started: HMMsearch
[2023-06-27 10:11:51,141] [INFO] Running command: hmmsearch --tblout GCA_026706455.1_ASM2670645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b77be32-3540-4767-9b5b-1d519eb54bee/dqc_reference/reference_markers.hmm GCA_026706455.1_ASM2670645v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:11:51,411] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:11:51,413] [INFO] Found 6/6 markers.
[2023-06-27 10:11:51,453] [INFO] Query marker FASTA was written to GCA_026706455.1_ASM2670645v1_genomic.fna/markers.fasta
[2023-06-27 10:11:51,453] [INFO] Task started: Blastn
[2023-06-27 10:11:51,453] [INFO] Running command: blastn -query GCA_026706455.1_ASM2670645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b77be32-3540-4767-9b5b-1d519eb54bee/dqc_reference/reference_markers.fasta -out GCA_026706455.1_ASM2670645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:11:52,097] [INFO] Task succeeded: Blastn
[2023-06-27 10:11:52,101] [INFO] Selected 16 target genomes.
[2023-06-27 10:11:52,102] [INFO] Target genome list was writen to GCA_026706455.1_ASM2670645v1_genomic.fna/target_genomes.txt
[2023-06-27 10:11:52,105] [INFO] Task started: fastANI
[2023-06-27 10:11:52,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbf7908-7519-442e-b39d-004c4fe141fa/GCA_026706455.1_ASM2670645v1_genomic.fna.gz --refList GCA_026706455.1_ASM2670645v1_genomic.fna/target_genomes.txt --output GCA_026706455.1_ASM2670645v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:12:02,684] [INFO] Task succeeded: fastANI
[2023-06-27 10:12:02,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b77be32-3540-4767-9b5b-1d519eb54bee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:12:02,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b77be32-3540-4767-9b5b-1d519eb54bee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:12:02,691] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:12:02,692] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 10:12:02,692] [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
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	74.541	50	1187	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 10:12:02,697] [INFO] DFAST Taxonomy check result was written to GCA_026706455.1_ASM2670645v1_genomic.fna/tc_result.tsv
[2023-06-27 10:12:02,698] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:12:02,698] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:12:02,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b77be32-3540-4767-9b5b-1d519eb54bee/dqc_reference/checkm_data
[2023-06-27 10:12:02,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:12:02,762] [INFO] Task started: CheckM
[2023-06-27 10:12:02,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026706455.1_ASM2670645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026706455.1_ASM2670645v1_genomic.fna/checkm_input GCA_026706455.1_ASM2670645v1_genomic.fna/checkm_result
[2023-06-27 10:12:37,170] [INFO] Task succeeded: CheckM
[2023-06-27 10:12:37,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 10:12:37,192] [INFO] ===== Completeness check finished =====
[2023-06-27 10:12:37,192] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:12:37,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026706455.1_ASM2670645v1_genomic.fna/markers.fasta)
[2023-06-27 10:12:37,193] [INFO] Task started: Blastn
[2023-06-27 10:12:37,193] [INFO] Running command: blastn -query GCA_026706455.1_ASM2670645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b77be32-3540-4767-9b5b-1d519eb54bee/dqc_reference/reference_markers_gtdb.fasta -out GCA_026706455.1_ASM2670645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:12:38,009] [INFO] Task succeeded: Blastn
[2023-06-27 10:12:38,023] [INFO] Selected 16 target genomes.
[2023-06-27 10:12:38,023] [INFO] Target genome list was writen to GCA_026706455.1_ASM2670645v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:12:38,149] [INFO] Task started: fastANI
[2023-06-27 10:12:38,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbf7908-7519-442e-b39d-004c4fe141fa/GCA_026706455.1_ASM2670645v1_genomic.fna.gz --refList GCA_026706455.1_ASM2670645v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026706455.1_ASM2670645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:12:52,317] [INFO] Task succeeded: fastANI
[2023-06-27 10:12:52,339] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 10:12:52,339] [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_011523545.1	s__UBA6055 sp011523545	80.9065	877	1187	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523705.1	s__UBA6055 sp011523705	80.4175	747	1187	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270545.1	s__UBA6055 sp012270545	80.1283	688	1187	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523735.1	s__UBA6055 sp011523735	79.3172	519	1187	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523515.1	s__UBA6055 sp011523515	78.8743	533	1187	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841405.1	s__UBA6055 sp009841405	78.8016	524	1187	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525385.1	s__UBA6055 sp011525385	78.2459	422	1187	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840575.1	s__UBA6055 sp009840575	77.7026	336	1187	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	99.83	99.79	0.96	0.95	8	-
GCA_016223085.1	s__CFX2 sp016223085	75.2431	56	1187	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717335.1	s__JADKFS01 sp016717335	74.7874	63	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JADKFS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 10:12:52,349] [INFO] GTDB search result was written to GCA_026706455.1_ASM2670645v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:12:52,350] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:12:52,353] [INFO] DFAST_QC result json was written to GCA_026706455.1_ASM2670645v1_genomic.fna/dqc_result.json
[2023-06-27 10:12:52,354] [INFO] DFAST_QC completed!
[2023-06-27 10:12:52,354] [INFO] Total running time: 0h1m14s