[2023-06-28 04:59:16,853] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:59:16,856] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:59:16,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg9018141b-204c-4269-aa0a-8fe3e821c72c/dqc_reference
[2023-06-28 04:59:18,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:59:18,033] [INFO] Task started: Prodigal
[2023-06-28 04:59:18,033] [INFO] Running command: gunzip -c /var/lib/cwl/stg29457007-1dce-45b3-bc5e-0de37b7e0ab4/GCA_017477845.1_ASM1747784v1_genomic.fna.gz | prodigal -d GCA_017477845.1_ASM1747784v1_genomic.fna/cds.fna -a GCA_017477845.1_ASM1747784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:59:20,240] [INFO] Task succeeded: Prodigal
[2023-06-28 04:59:20,240] [INFO] Task started: HMMsearch
[2023-06-28 04:59:20,240] [INFO] Running command: hmmsearch --tblout GCA_017477845.1_ASM1747784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9018141b-204c-4269-aa0a-8fe3e821c72c/dqc_reference/reference_markers.hmm GCA_017477845.1_ASM1747784v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:59:20,417] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:59:20,418] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg29457007-1dce-45b3-bc5e-0de37b7e0ab4/GCA_017477845.1_ASM1747784v1_genomic.fna.gz]
[2023-06-28 04:59:20,436] [INFO] Query marker FASTA was written to GCA_017477845.1_ASM1747784v1_genomic.fna/markers.fasta
[2023-06-28 04:59:20,436] [INFO] Task started: Blastn
[2023-06-28 04:59:20,436] [INFO] Running command: blastn -query GCA_017477845.1_ASM1747784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9018141b-204c-4269-aa0a-8fe3e821c72c/dqc_reference/reference_markers.fasta -out GCA_017477845.1_ASM1747784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:59:21,002] [INFO] Task succeeded: Blastn
[2023-06-28 04:59:21,017] [INFO] Selected 22 target genomes.
[2023-06-28 04:59:21,018] [INFO] Target genome list was writen to GCA_017477845.1_ASM1747784v1_genomic.fna/target_genomes.txt
[2023-06-28 04:59:21,019] [INFO] Task started: fastANI
[2023-06-28 04:59:21,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg29457007-1dce-45b3-bc5e-0de37b7e0ab4/GCA_017477845.1_ASM1747784v1_genomic.fna.gz --refList GCA_017477845.1_ASM1747784v1_genomic.fna/target_genomes.txt --output GCA_017477845.1_ASM1747784v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:59:29,061] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:29,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9018141b-204c-4269-aa0a-8fe3e821c72c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:59:29,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9018141b-204c-4269-aa0a-8fe3e821c72c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:59:29,063] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:59:29,063] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:59:29,063] [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
--------------------------------------------------------------------------------
[2023-06-28 04:59:29,065] [INFO] DFAST Taxonomy check result was written to GCA_017477845.1_ASM1747784v1_genomic.fna/tc_result.tsv
[2023-06-28 04:59:29,065] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:59:29,065] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:59:29,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9018141b-204c-4269-aa0a-8fe3e821c72c/dqc_reference/checkm_data
[2023-06-28 04:59:29,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:59:29,086] [INFO] Task started: CheckM
[2023-06-28 04:59:29,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017477845.1_ASM1747784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017477845.1_ASM1747784v1_genomic.fna/checkm_input GCA_017477845.1_ASM1747784v1_genomic.fna/checkm_result
[2023-06-28 04:59:43,306] [INFO] Task succeeded: CheckM
[2023-06-28 04:59:43,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:59:43,321] [INFO] ===== Completeness check finished =====
[2023-06-28 04:59:43,322] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:59:43,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017477845.1_ASM1747784v1_genomic.fna/markers.fasta)
[2023-06-28 04:59:43,322] [INFO] Task started: Blastn
[2023-06-28 04:59:43,322] [INFO] Running command: blastn -query GCA_017477845.1_ASM1747784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9018141b-204c-4269-aa0a-8fe3e821c72c/dqc_reference/reference_markers_gtdb.fasta -out GCA_017477845.1_ASM1747784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:59:44,144] [INFO] Task succeeded: Blastn
[2023-06-28 04:59:44,150] [INFO] Selected 12 target genomes.
[2023-06-28 04:59:44,150] [INFO] Target genome list was writen to GCA_017477845.1_ASM1747784v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:59:44,152] [INFO] Task started: fastANI
[2023-06-28 04:59:44,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg29457007-1dce-45b3-bc5e-0de37b7e0ab4/GCA_017477845.1_ASM1747784v1_genomic.fna.gz --refList GCA_017477845.1_ASM1747784v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017477845.1_ASM1747784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:59:47,195] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:47,205] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:59:47,205] [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_017477845.1	s__RUG13868 sp017477845	100.0	491	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13868	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902793375.1	s__RUG13868 sp902793375	79.3094	205	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017525035.1	s__RUG13868 sp017525035	79.2028	168	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767365.1	s__RUG13868 sp902767365	78.8137	195	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625395.1	s__RUG13868 sp017625395	78.3361	131	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541325.1	s__RUG11788 sp017541325	77.194	78	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11788	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432665.1	s__UBA3789 sp017432665	76.8096	50	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436255.1	s__CAG-1193 sp000436255	76.495	53	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1193	95.0	98.61	98.61	0.83	0.83	2	-
GCA_900542735.1	s__Scybalousia sp900542735	76.468	65	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	98.00	97.98	0.84	0.82	4	-
GCA_902801525.1	s__RUG14670 sp902801525	76.0799	59	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14670	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783435.1	s__UBA3789 sp902783435	75.8059	54	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 04:59:47,206] [INFO] GTDB search result was written to GCA_017477845.1_ASM1747784v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:59:47,207] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:59:47,210] [INFO] DFAST_QC result json was written to GCA_017477845.1_ASM1747784v1_genomic.fna/dqc_result.json
[2023-06-28 04:59:47,210] [INFO] DFAST_QC completed!
[2023-06-28 04:59:47,210] [INFO] Total running time: 0h0m30s