[2023-06-13 01:53:07,376] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:53:07,378] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:53:07,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e94316a-a8dc-49a2-adfe-95d305cf4694/dqc_reference
[2023-06-13 01:53:08,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:53:08,908] [INFO] Task started: Prodigal
[2023-06-13 01:53:08,909] [INFO] Running command: gunzip -c /var/lib/cwl/stga60df0aa-604d-4a16-b764-d15fa0ebeaaf/GCA_022564795.1_ASM2256479v1_genomic.fna.gz | prodigal -d GCA_022564795.1_ASM2256479v1_genomic.fna/cds.fna -a GCA_022564795.1_ASM2256479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:53:12,137] [INFO] Task succeeded: Prodigal
[2023-06-13 01:53:12,138] [INFO] Task started: HMMsearch
[2023-06-13 01:53:12,138] [INFO] Running command: hmmsearch --tblout GCA_022564795.1_ASM2256479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e94316a-a8dc-49a2-adfe-95d305cf4694/dqc_reference/reference_markers.hmm GCA_022564795.1_ASM2256479v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:53:12,378] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:53:12,379] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga60df0aa-604d-4a16-b764-d15fa0ebeaaf/GCA_022564795.1_ASM2256479v1_genomic.fna.gz]
[2023-06-13 01:53:12,402] [INFO] Query marker FASTA was written to GCA_022564795.1_ASM2256479v1_genomic.fna/markers.fasta
[2023-06-13 01:53:12,402] [INFO] Task started: Blastn
[2023-06-13 01:53:12,402] [INFO] Running command: blastn -query GCA_022564795.1_ASM2256479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e94316a-a8dc-49a2-adfe-95d305cf4694/dqc_reference/reference_markers.fasta -out GCA_022564795.1_ASM2256479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:53:13,007] [INFO] Task succeeded: Blastn
[2023-06-13 01:53:13,013] [INFO] Selected 19 target genomes.
[2023-06-13 01:53:13,013] [INFO] Target genome list was writen to GCA_022564795.1_ASM2256479v1_genomic.fna/target_genomes.txt
[2023-06-13 01:53:13,020] [INFO] Task started: fastANI
[2023-06-13 01:53:13,020] [INFO] Running command: fastANI --query /var/lib/cwl/stga60df0aa-604d-4a16-b764-d15fa0ebeaaf/GCA_022564795.1_ASM2256479v1_genomic.fna.gz --refList GCA_022564795.1_ASM2256479v1_genomic.fna/target_genomes.txt --output GCA_022564795.1_ASM2256479v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:53:28,364] [INFO] Task succeeded: fastANI
[2023-06-13 01:53:28,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e94316a-a8dc-49a2-adfe-95d305cf4694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:53:28,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e94316a-a8dc-49a2-adfe-95d305cf4694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:53:28,369] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:53:28,369] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 01:53:28,369] [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
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	74.6501	54	387	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:53:28,371] [INFO] DFAST Taxonomy check result was written to GCA_022564795.1_ASM2256479v1_genomic.fna/tc_result.tsv
[2023-06-13 01:53:28,373] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:53:28,373] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:53:28,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e94316a-a8dc-49a2-adfe-95d305cf4694/dqc_reference/checkm_data
[2023-06-13 01:53:28,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:53:28,396] [INFO] Task started: CheckM
[2023-06-13 01:53:28,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022564795.1_ASM2256479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022564795.1_ASM2256479v1_genomic.fna/checkm_input GCA_022564795.1_ASM2256479v1_genomic.fna/checkm_result
[2023-06-13 01:53:46,865] [INFO] Task succeeded: CheckM
[2023-06-13 01:53:46,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 32.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:53:46,887] [INFO] ===== Completeness check finished =====
[2023-06-13 01:53:46,887] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:53:46,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022564795.1_ASM2256479v1_genomic.fna/markers.fasta)
[2023-06-13 01:53:46,888] [INFO] Task started: Blastn
[2023-06-13 01:53:46,888] [INFO] Running command: blastn -query GCA_022564795.1_ASM2256479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e94316a-a8dc-49a2-adfe-95d305cf4694/dqc_reference/reference_markers_gtdb.fasta -out GCA_022564795.1_ASM2256479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:53:47,792] [INFO] Task succeeded: Blastn
[2023-06-13 01:53:47,798] [INFO] Selected 18 target genomes.
[2023-06-13 01:53:47,799] [INFO] Target genome list was writen to GCA_022564795.1_ASM2256479v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:53:47,812] [INFO] Task started: fastANI
[2023-06-13 01:53:47,812] [INFO] Running command: fastANI --query /var/lib/cwl/stga60df0aa-604d-4a16-b764-d15fa0ebeaaf/GCA_022564795.1_ASM2256479v1_genomic.fna.gz --refList GCA_022564795.1_ASM2256479v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022564795.1_ASM2256479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:53:56,854] [INFO] Task succeeded: fastANI
[2023-06-13 01:53:56,859] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:53:56,859] [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_001796995.1	s__RBG-16-68-14 sp001796995	78.8099	174	387	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__RBG-16-68-14;g__RBG-16-68-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228685.1	s__SZUA-185 sp003228685	78.2284	145	387	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__RBG-16-68-14;g__SZUA-185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478665.1	s__JADMII01 sp015478665	76.5837	77	387	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__DSTF01;f__JACRBR01;g__JADMII01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:53:56,861] [INFO] GTDB search result was written to GCA_022564795.1_ASM2256479v1_genomic.fna/result_gtdb.tsv
[2023-06-13 01:53:56,862] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:53:56,866] [INFO] DFAST_QC result json was written to GCA_022564795.1_ASM2256479v1_genomic.fna/dqc_result.json
[2023-06-13 01:53:56,866] [INFO] DFAST_QC completed!
[2023-06-13 01:53:56,866] [INFO] Total running time: 0h0m49s