[2023-03-16 02:38:04,998] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,999] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg175a4062-7903-4b00-8031-3e44e129b494/dqc_reference
[2023-03-16 02:38:06,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,238] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,238] [INFO] Running command: cat /var/lib/cwl/stg8134dea3-7f3c-4889-b0ce-1249ef960368/OceanDNA-b46405.fa | prodigal -d OceanDNA-b46405/cds.fna -a OceanDNA-b46405/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:29,153] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:29,153] [INFO] Task started: HMMsearch
[2023-03-16 02:38:29,153] [INFO] Running command: hmmsearch --tblout OceanDNA-b46405/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg175a4062-7903-4b00-8031-3e44e129b494/dqc_reference/reference_markers.hmm OceanDNA-b46405/protein.faa > /dev/null
[2023-03-16 02:38:29,313] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:29,314] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8134dea3-7f3c-4889-b0ce-1249ef960368/OceanDNA-b46405.fa]
[2023-03-16 02:38:29,334] [INFO] Query marker FASTA was written to OceanDNA-b46405/markers.fasta
[2023-03-16 02:38:29,334] [INFO] Task started: Blastn
[2023-03-16 02:38:29,334] [INFO] Running command: blastn -query OceanDNA-b46405/markers.fasta -db /var/lib/cwl/stg175a4062-7903-4b00-8031-3e44e129b494/dqc_reference/reference_markers.fasta -out OceanDNA-b46405/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:29,863] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:29,864] [INFO] Selected 15 target genomes.
[2023-03-16 02:38:29,864] [INFO] Target genome list was writen to OceanDNA-b46405/target_genomes.txt
[2023-03-16 02:38:29,877] [INFO] Task started: fastANI
[2023-03-16 02:38:29,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg8134dea3-7f3c-4889-b0ce-1249ef960368/OceanDNA-b46405.fa --refList OceanDNA-b46405/target_genomes.txt --output OceanDNA-b46405/fastani_result.tsv --threads 1
[2023-03-16 02:38:42,350] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:42,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg175a4062-7903-4b00-8031-3e44e129b494/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:42,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg175a4062-7903-4b00-8031-3e44e129b494/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:42,351] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:42,351] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 02:38:42,351] [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
--------------------------------------------------------------------------------
[2023-03-16 02:38:42,351] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46405/tc_result.tsv
[2023-03-16 02:38:42,351] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:42,351] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:42,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg175a4062-7903-4b00-8031-3e44e129b494/dqc_reference/checkm_data
[2023-03-16 02:38:42,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:42,359] [INFO] Task started: CheckM
[2023-03-16 02:38:42,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46405/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46405/checkm_input OceanDNA-b46405/checkm_result
[2023-03-16 02:39:40,703] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:40,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.38%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:40,706] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:40,706] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:40,706] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46405/markers.fasta)
[2023-03-16 02:39:40,706] [INFO] Task started: Blastn
[2023-03-16 02:39:40,706] [INFO] Running command: blastn -query OceanDNA-b46405/markers.fasta -db /var/lib/cwl/stg175a4062-7903-4b00-8031-3e44e129b494/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46405/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:41,409] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:41,410] [INFO] Selected 7 target genomes.
[2023-03-16 02:39:41,410] [INFO] Target genome list was writen to OceanDNA-b46405/target_genomes_gtdb.txt
[2023-03-16 02:39:41,589] [INFO] Task started: fastANI
[2023-03-16 02:39:41,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg8134dea3-7f3c-4889-b0ce-1249ef960368/OceanDNA-b46405.fa --refList OceanDNA-b46405/target_genomes_gtdb.txt --output OceanDNA-b46405/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:46,062] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:46,067] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 02:39:46,067] [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_003972865.1	s__UBA1096 sp003972865	87.3197	446	722	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382705.1	s__UBA1096 sp014382705	84.7012	550	722	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658765.1	s__UBA1096 sp015658765	84.6423	350	722	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674955.1	s__UBA1096 sp018674955	84.3576	494	722	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.88	98.74	0.86	0.81	14	-
GCA_002686755.1	s__UBA1096 sp002686755	83.7544	476	722	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299785.1	s__UBA1096 sp002299785	82.2343	359	722	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453165.1	s__UBA1096 sp002453165	78.6389	256	722	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	96.70	95.18	0.81	0.76	7	-
--------------------------------------------------------------------------------
[2023-03-16 02:39:46,067] [INFO] GTDB search result was written to OceanDNA-b46405/result_gtdb.tsv
[2023-03-16 02:39:46,067] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:46,068] [INFO] DFAST_QC result json was written to OceanDNA-b46405/dqc_result.json
[2023-03-16 02:39:46,068] [INFO] DFAST_QC completed!
[2023-03-16 02:39:46,068] [INFO] Total running time: 0h1m41s