[2023-06-19 08:29:18,706] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:29:18,708] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:29:18,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ab8aa8f-bacc-44c7-b77d-008695697e73/dqc_reference
[2023-06-19 08:29:19,881] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:29:19,881] [INFO] Task started: Prodigal
[2023-06-19 08:29:19,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg3353bebe-95ca-43b4-98ad-39573a8e8507/GCA_018655785.1_ASM1865578v1_genomic.fna.gz | prodigal -d GCA_018655785.1_ASM1865578v1_genomic.fna/cds.fna -a GCA_018655785.1_ASM1865578v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:29:22,470] [INFO] Task succeeded: Prodigal
[2023-06-19 08:29:22,471] [INFO] Task started: HMMsearch
[2023-06-19 08:29:22,471] [INFO] Running command: hmmsearch --tblout GCA_018655785.1_ASM1865578v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ab8aa8f-bacc-44c7-b77d-008695697e73/dqc_reference/reference_markers.hmm GCA_018655785.1_ASM1865578v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:29:22,631] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:29:22,631] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3353bebe-95ca-43b4-98ad-39573a8e8507/GCA_018655785.1_ASM1865578v1_genomic.fna.gz]
[2023-06-19 08:29:22,655] [INFO] Query marker FASTA was written to GCA_018655785.1_ASM1865578v1_genomic.fna/markers.fasta
[2023-06-19 08:29:22,655] [INFO] Task started: Blastn
[2023-06-19 08:29:22,655] [INFO] Running command: blastn -query GCA_018655785.1_ASM1865578v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ab8aa8f-bacc-44c7-b77d-008695697e73/dqc_reference/reference_markers.fasta -out GCA_018655785.1_ASM1865578v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:29:23,197] [INFO] Task succeeded: Blastn
[2023-06-19 08:29:23,200] [INFO] Selected 16 target genomes.
[2023-06-19 08:29:23,201] [INFO] Target genome list was writen to GCA_018655785.1_ASM1865578v1_genomic.fna/target_genomes.txt
[2023-06-19 08:29:23,204] [INFO] Task started: fastANI
[2023-06-19 08:29:23,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg3353bebe-95ca-43b4-98ad-39573a8e8507/GCA_018655785.1_ASM1865578v1_genomic.fna.gz --refList GCA_018655785.1_ASM1865578v1_genomic.fna/target_genomes.txt --output GCA_018655785.1_ASM1865578v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:29:29,700] [INFO] Task succeeded: fastANI
[2023-06-19 08:29:29,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ab8aa8f-bacc-44c7-b77d-008695697e73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:29:29,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ab8aa8f-bacc-44c7-b77d-008695697e73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:29:29,702] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:29:29,702] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:29:29,702] [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
--------------------------------------------------------------------------------
[2023-06-19 08:29:29,705] [INFO] DFAST Taxonomy check result was written to GCA_018655785.1_ASM1865578v1_genomic.fna/tc_result.tsv
[2023-06-19 08:29:29,705] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:29:29,706] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:29:29,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ab8aa8f-bacc-44c7-b77d-008695697e73/dqc_reference/checkm_data
[2023-06-19 08:29:29,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:29:29,731] [INFO] Task started: CheckM
[2023-06-19 08:29:29,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018655785.1_ASM1865578v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018655785.1_ASM1865578v1_genomic.fna/checkm_input GCA_018655785.1_ASM1865578v1_genomic.fna/checkm_result
[2023-06-19 08:29:45,326] [INFO] Task succeeded: CheckM
[2023-06-19 08:29:45,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.82%
Contamintation: 6.64%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-06-19 08:29:45,357] [INFO] ===== Completeness check finished =====
[2023-06-19 08:29:45,357] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:29:45,357] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018655785.1_ASM1865578v1_genomic.fna/markers.fasta)
[2023-06-19 08:29:45,357] [INFO] Task started: Blastn
[2023-06-19 08:29:45,357] [INFO] Running command: blastn -query GCA_018655785.1_ASM1865578v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ab8aa8f-bacc-44c7-b77d-008695697e73/dqc_reference/reference_markers_gtdb.fasta -out GCA_018655785.1_ASM1865578v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:29:46,150] [INFO] Task succeeded: Blastn
[2023-06-19 08:29:46,154] [INFO] Selected 24 target genomes.
[2023-06-19 08:29:46,154] [INFO] Target genome list was writen to GCA_018655785.1_ASM1865578v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:29:46,244] [INFO] Task started: fastANI
[2023-06-19 08:29:46,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg3353bebe-95ca-43b4-98ad-39573a8e8507/GCA_018655785.1_ASM1865578v1_genomic.fna.gz --refList GCA_018655785.1_ASM1865578v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018655785.1_ASM1865578v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:29:52,505] [INFO] Task succeeded: fastANI
[2023-06-19 08:29:52,511] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 08:29:52,511] [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_015660425.1	s__TMED109 sp015660425	83.706	154	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684605.1	s__TMED109 sp002684605	82.7176	228	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171375.1	s__TMED109 sp002171375	78.2045	115	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	98.96	97.53	0.84	0.73	4	-
GCA_002720535.1	s__TMED109 sp002720535	77.7694	139	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	95.89	95.27	0.82	0.81	3	-
GCA_002715265.1	s__GCA-002727615 sp002715265	76.6278	85	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__GCA-002727615	95.0	98.23	98.23	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-19 08:29:52,514] [INFO] GTDB search result was written to GCA_018655785.1_ASM1865578v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:29:52,515] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:29:52,517] [INFO] DFAST_QC result json was written to GCA_018655785.1_ASM1865578v1_genomic.fna/dqc_result.json
[2023-06-19 08:29:52,517] [INFO] DFAST_QC completed!
[2023-06-19 08:29:52,517] [INFO] Total running time: 0h0m34s