[2023-06-13 16:35:21,786] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:35:21,791] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:35:21,792] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdb993aa-da77-47c9-8a9c-a3297c771742/dqc_reference
[2023-06-13 16:35:23,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:35:23,137] [INFO] Task started: Prodigal
[2023-06-13 16:35:23,137] [INFO] Running command: gunzip -c /var/lib/cwl/stga9314c97-4c63-47cb-b566-001d7ca6b127/GCA_022072175.1_ASM2207217v1_genomic.fna.gz | prodigal -d GCA_022072175.1_ASM2207217v1_genomic.fna/cds.fna -a GCA_022072175.1_ASM2207217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:35:35,362] [INFO] Task succeeded: Prodigal
[2023-06-13 16:35:35,363] [INFO] Task started: HMMsearch
[2023-06-13 16:35:35,363] [INFO] Running command: hmmsearch --tblout GCA_022072175.1_ASM2207217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdb993aa-da77-47c9-8a9c-a3297c771742/dqc_reference/reference_markers.hmm GCA_022072175.1_ASM2207217v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:35:35,632] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:35:35,634] [INFO] Found 6/6 markers.
[2023-06-13 16:35:35,670] [INFO] Query marker FASTA was written to GCA_022072175.1_ASM2207217v1_genomic.fna/markers.fasta
[2023-06-13 16:35:35,670] [INFO] Task started: Blastn
[2023-06-13 16:35:35,670] [INFO] Running command: blastn -query GCA_022072175.1_ASM2207217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdb993aa-da77-47c9-8a9c-a3297c771742/dqc_reference/reference_markers.fasta -out GCA_022072175.1_ASM2207217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:35:36,329] [INFO] Task succeeded: Blastn
[2023-06-13 16:35:36,334] [INFO] Selected 26 target genomes.
[2023-06-13 16:35:36,335] [INFO] Target genome list was writen to GCA_022072175.1_ASM2207217v1_genomic.fna/target_genomes.txt
[2023-06-13 16:35:36,351] [INFO] Task started: fastANI
[2023-06-13 16:35:36,352] [INFO] Running command: fastANI --query /var/lib/cwl/stga9314c97-4c63-47cb-b566-001d7ca6b127/GCA_022072175.1_ASM2207217v1_genomic.fna.gz --refList GCA_022072175.1_ASM2207217v1_genomic.fna/target_genomes.txt --output GCA_022072175.1_ASM2207217v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:35:54,421] [INFO] Task succeeded: fastANI
[2023-06-13 16:35:54,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdb993aa-da77-47c9-8a9c-a3297c771742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:35:54,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdb993aa-da77-47c9-8a9c-a3297c771742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:35:54,426] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:35:54,427] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 16:35:54,427] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.2313	66	895	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.1459	51	895	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 16:35:54,429] [INFO] DFAST Taxonomy check result was written to GCA_022072175.1_ASM2207217v1_genomic.fna/tc_result.tsv
[2023-06-13 16:35:54,429] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:35:54,430] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:35:54,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdb993aa-da77-47c9-8a9c-a3297c771742/dqc_reference/checkm_data
[2023-06-13 16:35:54,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:35:54,465] [INFO] Task started: CheckM
[2023-06-13 16:35:54,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022072175.1_ASM2207217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022072175.1_ASM2207217v1_genomic.fna/checkm_input GCA_022072175.1_ASM2207217v1_genomic.fna/checkm_result
[2023-06-13 16:36:33,387] [INFO] Task succeeded: CheckM
[2023-06-13 16:36:33,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 16:36:33,412] [INFO] ===== Completeness check finished =====
[2023-06-13 16:36:33,412] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:36:33,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022072175.1_ASM2207217v1_genomic.fna/markers.fasta)
[2023-06-13 16:36:33,413] [INFO] Task started: Blastn
[2023-06-13 16:36:33,413] [INFO] Running command: blastn -query GCA_022072175.1_ASM2207217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdb993aa-da77-47c9-8a9c-a3297c771742/dqc_reference/reference_markers_gtdb.fasta -out GCA_022072175.1_ASM2207217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:36:34,361] [INFO] Task succeeded: Blastn
[2023-06-13 16:36:34,365] [INFO] Selected 25 target genomes.
[2023-06-13 16:36:34,366] [INFO] Target genome list was writen to GCA_022072175.1_ASM2207217v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:36:34,397] [INFO] Task started: fastANI
[2023-06-13 16:36:34,398] [INFO] Running command: fastANI --query /var/lib/cwl/stga9314c97-4c63-47cb-b566-001d7ca6b127/GCA_022072175.1_ASM2207217v1_genomic.fna.gz --refList GCA_022072175.1_ASM2207217v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022072175.1_ASM2207217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:36:46,740] [INFO] Task succeeded: fastANI
[2023-06-13 16:36:46,747] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 16:36:46,747] [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_016197155.1	s__JACQQX01 sp016197155	77.0283	68	895	d__Bacteria;p__Omnitrophota;c__Koll11;o__2-02-FULL-51-18;f__2-02-FULL-51-18;g__JACQQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016180585.1	s__JACPAX01 sp016180585	76.5243	68	895	d__Bacteria;p__Omnitrophota;c__Koll11;o__2-02-FULL-51-18;f__2-02-FULL-51-18;g__JACPAX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 16:36:46,750] [INFO] GTDB search result was written to GCA_022072175.1_ASM2207217v1_genomic.fna/result_gtdb.tsv
[2023-06-13 16:36:46,750] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:36:46,753] [INFO] DFAST_QC result json was written to GCA_022072175.1_ASM2207217v1_genomic.fna/dqc_result.json
[2023-06-13 16:36:46,753] [INFO] DFAST_QC completed!
[2023-06-13 16:36:46,753] [INFO] Total running time: 0h1m25s