[2023-06-28 16:24:11,905] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:24:11,907] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:24:11,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg919ab6a5-b076-4dcb-abb3-f7c554d67043/dqc_reference
[2023-06-28 16:24:13,071] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:24:13,071] [INFO] Task started: Prodigal
[2023-06-28 16:24:13,072] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f0eaeab-943e-4444-b031-be5cfbc70d72/GCA_017480965.1_ASM1748096v1_genomic.fna.gz | prodigal -d GCA_017480965.1_ASM1748096v1_genomic.fna/cds.fna -a GCA_017480965.1_ASM1748096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:24:17,611] [INFO] Task succeeded: Prodigal
[2023-06-28 16:24:17,611] [INFO] Task started: HMMsearch
[2023-06-28 16:24:17,611] [INFO] Running command: hmmsearch --tblout GCA_017480965.1_ASM1748096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg919ab6a5-b076-4dcb-abb3-f7c554d67043/dqc_reference/reference_markers.hmm GCA_017480965.1_ASM1748096v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:24:17,802] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:24:17,803] [INFO] Found 6/6 markers.
[2023-06-28 16:24:17,825] [INFO] Query marker FASTA was written to GCA_017480965.1_ASM1748096v1_genomic.fna/markers.fasta
[2023-06-28 16:24:17,826] [INFO] Task started: Blastn
[2023-06-28 16:24:17,826] [INFO] Running command: blastn -query GCA_017480965.1_ASM1748096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg919ab6a5-b076-4dcb-abb3-f7c554d67043/dqc_reference/reference_markers.fasta -out GCA_017480965.1_ASM1748096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:24:18,454] [INFO] Task succeeded: Blastn
[2023-06-28 16:24:18,458] [INFO] Selected 26 target genomes.
[2023-06-28 16:24:18,458] [INFO] Target genome list was writen to GCA_017480965.1_ASM1748096v1_genomic.fna/target_genomes.txt
[2023-06-28 16:24:18,459] [INFO] Task started: fastANI
[2023-06-28 16:24:18,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f0eaeab-943e-4444-b031-be5cfbc70d72/GCA_017480965.1_ASM1748096v1_genomic.fna.gz --refList GCA_017480965.1_ASM1748096v1_genomic.fna/target_genomes.txt --output GCA_017480965.1_ASM1748096v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:24:33,248] [INFO] Task succeeded: fastANI
[2023-06-28 16:24:33,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg919ab6a5-b076-4dcb-abb3-f7c554d67043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:24:33,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg919ab6a5-b076-4dcb-abb3-f7c554d67043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:24:33,250] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:24:33,251] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:24:33,251] [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 16:24:33,253] [INFO] DFAST Taxonomy check result was written to GCA_017480965.1_ASM1748096v1_genomic.fna/tc_result.tsv
[2023-06-28 16:24:33,253] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:24:33,253] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:24:33,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg919ab6a5-b076-4dcb-abb3-f7c554d67043/dqc_reference/checkm_data
[2023-06-28 16:24:33,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:24:33,277] [INFO] Task started: CheckM
[2023-06-28 16:24:33,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017480965.1_ASM1748096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017480965.1_ASM1748096v1_genomic.fna/checkm_input GCA_017480965.1_ASM1748096v1_genomic.fna/checkm_result
[2023-06-28 16:24:52,897] [INFO] Task succeeded: CheckM
[2023-06-28 16:24:52,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 16:24:52,918] [INFO] ===== Completeness check finished =====
[2023-06-28 16:24:52,918] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:24:52,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017480965.1_ASM1748096v1_genomic.fna/markers.fasta)
[2023-06-28 16:24:52,919] [INFO] Task started: Blastn
[2023-06-28 16:24:52,919] [INFO] Running command: blastn -query GCA_017480965.1_ASM1748096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg919ab6a5-b076-4dcb-abb3-f7c554d67043/dqc_reference/reference_markers_gtdb.fasta -out GCA_017480965.1_ASM1748096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:24:54,042] [INFO] Task succeeded: Blastn
[2023-06-28 16:24:54,046] [INFO] Selected 12 target genomes.
[2023-06-28 16:24:54,046] [INFO] Target genome list was writen to GCA_017480965.1_ASM1748096v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:24:54,048] [INFO] Task started: fastANI
[2023-06-28 16:24:54,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f0eaeab-943e-4444-b031-be5cfbc70d72/GCA_017480965.1_ASM1748096v1_genomic.fna.gz --refList GCA_017480965.1_ASM1748096v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017480965.1_ASM1748096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:24:58,224] [INFO] Task succeeded: fastANI
[2023-06-28 16:24:58,234] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:24:58,235] [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_017935485.1	s__MGBC133411 sp017935485	98.3334	487	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	98.32	98.32	0.87	0.87	2	conclusive
GCA_910585375.1	s__MGBC133411 sp910585375	93.4434	495	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540425.1	s__MGBC133411 sp900540425	78.0356	178	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	99.13	99.08	0.91	0.88	3	-
GCA_001917125.1	s__Scatocola faecipullorum	77.9092	148	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	98.98	98.59	0.91	0.85	10	-
GCA_017626035.1	s__JAGAJR01 sp017626035	77.8366	116	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__JAGAJR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018362935.1	s__CAZU01 sp018362935	77.755	135	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762585.1	s__HGM16780 sp900762585	77.7037	111	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__HGM16780	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436375.1	s__Scatacola_A faecigallinarum	77.4985	135	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatacola_A	95.0	97.40	96.59	0.91	0.88	10	-
GCA_000432275.1	s__CAZU01 sp000432275	77.4549	115	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	98.86	98.76	0.93	0.90	5	-
GCA_900538765.1	s__HGM16780 sp900538765	77.1066	127	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__HGM16780	95.0	98.94	98.77	0.94	0.91	4	-
GCA_905210515.1	s__CAJLXD01 sp905210515	77.0644	86	574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAJLXD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:24:58,239] [INFO] GTDB search result was written to GCA_017480965.1_ASM1748096v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:24:58,240] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:24:58,243] [INFO] DFAST_QC result json was written to GCA_017480965.1_ASM1748096v1_genomic.fna/dqc_result.json
[2023-06-28 16:24:58,243] [INFO] DFAST_QC completed!
[2023-06-28 16:24:58,243] [INFO] Total running time: 0h0m46s