[2023-06-30 21:54:33,325] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:54:33,327] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:54:33,328] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a6af6d4-f856-44f2-844f-acb96180047f/dqc_reference
[2023-06-30 21:54:35,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:54:35,796] [INFO] Task started: Prodigal
[2023-06-30 21:54:35,796] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfa7f4f8-10c3-4cd2-a93e-66eba4570b7a/GCA_024408075.1_ASM2440807v1_genomic.fna.gz | prodigal -d GCA_024408075.1_ASM2440807v1_genomic.fna/cds.fna -a GCA_024408075.1_ASM2440807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:54:37,529] [INFO] Task succeeded: Prodigal
[2023-06-30 21:54:37,530] [INFO] Task started: HMMsearch
[2023-06-30 21:54:37,530] [INFO] Running command: hmmsearch --tblout GCA_024408075.1_ASM2440807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a6af6d4-f856-44f2-844f-acb96180047f/dqc_reference/reference_markers.hmm GCA_024408075.1_ASM2440807v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:54:37,852] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:54:37,853] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdfa7f4f8-10c3-4cd2-a93e-66eba4570b7a/GCA_024408075.1_ASM2440807v1_genomic.fna.gz]
[2023-06-30 21:54:37,870] [INFO] Query marker FASTA was written to GCA_024408075.1_ASM2440807v1_genomic.fna/markers.fasta
[2023-06-30 21:54:37,870] [INFO] Task started: Blastn
[2023-06-30 21:54:37,870] [INFO] Running command: blastn -query GCA_024408075.1_ASM2440807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a6af6d4-f856-44f2-844f-acb96180047f/dqc_reference/reference_markers.fasta -out GCA_024408075.1_ASM2440807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:54:40,214] [INFO] Task succeeded: Blastn
[2023-06-30 21:54:40,219] [INFO] Selected 20 target genomes.
[2023-06-30 21:54:40,220] [INFO] Target genome list was writen to GCA_024408075.1_ASM2440807v1_genomic.fna/target_genomes.txt
[2023-06-30 21:54:40,225] [INFO] Task started: fastANI
[2023-06-30 21:54:40,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfa7f4f8-10c3-4cd2-a93e-66eba4570b7a/GCA_024408075.1_ASM2440807v1_genomic.fna.gz --refList GCA_024408075.1_ASM2440807v1_genomic.fna/target_genomes.txt --output GCA_024408075.1_ASM2440807v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:54:47,326] [INFO] Task succeeded: fastANI
[2023-06-30 21:54:47,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a6af6d4-f856-44f2-844f-acb96180047f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:54:47,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a6af6d4-f856-44f2-844f-acb96180047f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:54:47,329] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:54:47,329] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 21:54:47,330] [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
--------------------------------------------------------------------------------
[2023-06-30 21:54:47,332] [INFO] DFAST Taxonomy check result was written to GCA_024408075.1_ASM2440807v1_genomic.fna/tc_result.tsv
[2023-06-30 21:54:47,333] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:54:47,333] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:54:47,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a6af6d4-f856-44f2-844f-acb96180047f/dqc_reference/checkm_data
[2023-06-30 21:54:47,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:54:47,355] [INFO] Task started: CheckM
[2023-06-30 21:54:47,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024408075.1_ASM2440807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024408075.1_ASM2440807v1_genomic.fna/checkm_input GCA_024408075.1_ASM2440807v1_genomic.fna/checkm_result
[2023-06-30 21:55:01,288] [INFO] Task succeeded: CheckM
[2023-06-30 21:55:01,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:55:01,310] [INFO] ===== Completeness check finished =====
[2023-06-30 21:55:01,311] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:55:01,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024408075.1_ASM2440807v1_genomic.fna/markers.fasta)
[2023-06-30 21:55:01,311] [INFO] Task started: Blastn
[2023-06-30 21:55:01,311] [INFO] Running command: blastn -query GCA_024408075.1_ASM2440807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a6af6d4-f856-44f2-844f-acb96180047f/dqc_reference/reference_markers_gtdb.fasta -out GCA_024408075.1_ASM2440807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:55:02,020] [INFO] Task succeeded: Blastn
[2023-06-30 21:55:02,024] [INFO] Selected 20 target genomes.
[2023-06-30 21:55:02,024] [INFO] Target genome list was writen to GCA_024408075.1_ASM2440807v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:55:02,037] [INFO] Task started: fastANI
[2023-06-30 21:55:02,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfa7f4f8-10c3-4cd2-a93e-66eba4570b7a/GCA_024408075.1_ASM2440807v1_genomic.fna.gz --refList GCA_024408075.1_ASM2440807v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024408075.1_ASM2440807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:55:06,470] [INFO] Task succeeded: fastANI
[2023-06-30 21:55:06,487] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 21:55:06,488] [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_900314865.1	s__UBA2450 sp900314865	79.2716	77	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902800355.1	s__UBA2450 sp902800355	79.0027	81	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017635565.1	s__UBA2450 sp017635565	78.809	53	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769185.1	s__UBA2450 sp902769185	78.7045	89	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	95.75	95.75	0.77	0.77	2	-
GCA_902803285.1	s__UBA2450 sp902803285	78.6912	80	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	98.57	98.57	0.85	0.85	2	-
GCA_002353275.1	s__UBA2450 sp002353275	78.6511	86	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802905.1	s__UBA2450 sp902802905	78.6393	75	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800645.1	s__UBA2450 sp902800645	78.6328	83	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800025.1	s__UBA2450 sp902800025	78.5016	79	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	97.35	97.35	0.90	0.90	2	-
GCA_002342545.1	s__UBA2450 sp002342545	78.4517	96	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447165.1	s__UBA2450 sp017447165	78.3665	86	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800905.1	s__UBA2450 sp902800905	78.3236	81	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797795.1	s__UBA2450 sp902797795	78.2173	70	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002373085.1	s__UBA2450 sp002373085	77.8902	50	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	95.60	95.60	0.78	0.78	2	-
GCA_002392945.1	s__UBA2450 sp002392945	77.8577	69	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 21:55:06,490] [INFO] GTDB search result was written to GCA_024408075.1_ASM2440807v1_genomic.fna/result_gtdb.tsv
[2023-06-30 21:55:06,491] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:55:06,494] [INFO] DFAST_QC result json was written to GCA_024408075.1_ASM2440807v1_genomic.fna/dqc_result.json
[2023-06-30 21:55:06,495] [INFO] DFAST_QC completed!
[2023-06-30 21:55:06,495] [INFO] Total running time: 0h0m33s