[2023-06-19 00:05:15,023] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:05:15,025] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:05:15,025] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe252791-0c09-4de2-aa6e-dedba3f7534c/dqc_reference
[2023-06-19 00:05:16,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:05:16,345] [INFO] Task started: Prodigal
[2023-06-19 00:05:16,346] [INFO] Running command: gunzip -c /var/lib/cwl/stg11fa62d4-5d44-4ada-90d8-ea012179f472/GCA_018267355.1_ASM1826735v1_genomic.fna.gz | prodigal -d GCA_018267355.1_ASM1826735v1_genomic.fna/cds.fna -a GCA_018267355.1_ASM1826735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:05:31,288] [INFO] Task succeeded: Prodigal
[2023-06-19 00:05:31,289] [INFO] Task started: HMMsearch
[2023-06-19 00:05:31,289] [INFO] Running command: hmmsearch --tblout GCA_018267355.1_ASM1826735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe252791-0c09-4de2-aa6e-dedba3f7534c/dqc_reference/reference_markers.hmm GCA_018267355.1_ASM1826735v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:05:31,563] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:05:31,566] [INFO] Found 6/6 markers.
[2023-06-19 00:05:31,626] [INFO] Query marker FASTA was written to GCA_018267355.1_ASM1826735v1_genomic.fna/markers.fasta
[2023-06-19 00:05:31,627] [INFO] Task started: Blastn
[2023-06-19 00:05:31,627] [INFO] Running command: blastn -query GCA_018267355.1_ASM1826735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe252791-0c09-4de2-aa6e-dedba3f7534c/dqc_reference/reference_markers.fasta -out GCA_018267355.1_ASM1826735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:05:32,206] [INFO] Task succeeded: Blastn
[2023-06-19 00:05:32,217] [INFO] Selected 23 target genomes.
[2023-06-19 00:05:32,217] [INFO] Target genome list was writen to GCA_018267355.1_ASM1826735v1_genomic.fna/target_genomes.txt
[2023-06-19 00:05:32,224] [INFO] Task started: fastANI
[2023-06-19 00:05:32,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg11fa62d4-5d44-4ada-90d8-ea012179f472/GCA_018267355.1_ASM1826735v1_genomic.fna.gz --refList GCA_018267355.1_ASM1826735v1_genomic.fna/target_genomes.txt --output GCA_018267355.1_ASM1826735v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:05:52,687] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:52,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe252791-0c09-4de2-aa6e-dedba3f7534c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:05:52,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe252791-0c09-4de2-aa6e-dedba3f7534c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:05:52,691] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:05:52,691] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 00:05:52,692] [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 00:05:52,695] [INFO] DFAST Taxonomy check result was written to GCA_018267355.1_ASM1826735v1_genomic.fna/tc_result.tsv
[2023-06-19 00:05:52,703] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:05:52,704] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:05:52,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe252791-0c09-4de2-aa6e-dedba3f7534c/dqc_reference/checkm_data
[2023-06-19 00:05:52,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:05:52,755] [INFO] Task started: CheckM
[2023-06-19 00:05:52,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018267355.1_ASM1826735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018267355.1_ASM1826735v1_genomic.fna/checkm_input GCA_018267355.1_ASM1826735v1_genomic.fna/checkm_result
[2023-06-19 00:06:39,192] [INFO] Task succeeded: CheckM
[2023-06-19 00:06:39,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:06:39,260] [INFO] ===== Completeness check finished =====
[2023-06-19 00:06:39,261] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:06:39,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018267355.1_ASM1826735v1_genomic.fna/markers.fasta)
[2023-06-19 00:06:39,261] [INFO] Task started: Blastn
[2023-06-19 00:06:39,262] [INFO] Running command: blastn -query GCA_018267355.1_ASM1826735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe252791-0c09-4de2-aa6e-dedba3f7534c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018267355.1_ASM1826735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:06:40,024] [INFO] Task succeeded: Blastn
[2023-06-19 00:06:40,031] [INFO] Selected 11 target genomes.
[2023-06-19 00:06:40,031] [INFO] Target genome list was writen to GCA_018267355.1_ASM1826735v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:06:40,062] [INFO] Task started: fastANI
[2023-06-19 00:06:40,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg11fa62d4-5d44-4ada-90d8-ea012179f472/GCA_018267355.1_ASM1826735v1_genomic.fna.gz --refList GCA_018267355.1_ASM1826735v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018267355.1_ASM1826735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:06:48,082] [INFO] Task succeeded: fastANI
[2023-06-19 00:06:48,090] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:06:48,091] [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_018267355.1	s__UBA1941 sp018267355	99.9999	806	825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__LD1;g__UBA1941	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018267385.1	s__UBA1941 sp018267385	94.4183	734	825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__LD1;g__UBA1941	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336805.1	s__UBA1941 sp002336805	83.9755	592	825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__LD1;g__UBA1941	95.0	99.99	99.99	0.92	0.92	2	-
GCA_018267365.1	s__UBA1941 sp018267365	82.6556	647	825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__LD1;g__UBA1941	95.0	97.17	97.17	0.89	0.89	2	-
GCA_003165135.1	s__UBA1941 sp003165135	76.6024	83	825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__LD1;g__UBA1941	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917755.1	s__UBA1941 sp903917755	76.2973	94	825	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__LD1;g__UBA1941	95.0	99.86	99.86	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-19 00:06:48,093] [INFO] GTDB search result was written to GCA_018267355.1_ASM1826735v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:06:48,093] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:06:48,096] [INFO] DFAST_QC result json was written to GCA_018267355.1_ASM1826735v1_genomic.fna/dqc_result.json
[2023-06-19 00:06:48,096] [INFO] DFAST_QC completed!
[2023-06-19 00:06:48,096] [INFO] Total running time: 0h1m33s