[2023-03-17 01:23:45,143] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,143] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,143] [INFO] DQC Reference Directory: /var/lib/cwl/stge74600f1-6e3f-4e4a-866f-25a06c5488af/dqc_reference
[2023-03-17 01:23:46,318] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,318] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,318] [INFO] Running command: cat /var/lib/cwl/stg9594123a-c35c-4379-ba80-b0c82817188c/OceanDNA-b45554.fa | prodigal -d OceanDNA-b45554/cds.fna -a OceanDNA-b45554/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:24:01,118] [INFO] Task succeeded: Prodigal
[2023-03-17 01:24:01,118] [INFO] Task started: HMMsearch
[2023-03-17 01:24:01,118] [INFO] Running command: hmmsearch --tblout OceanDNA-b45554/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge74600f1-6e3f-4e4a-866f-25a06c5488af/dqc_reference/reference_markers.hmm OceanDNA-b45554/protein.faa > /dev/null
[2023-03-17 01:24:01,281] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:24:01,281] [INFO] Found 6/6 markers.
[2023-03-17 01:24:01,295] [INFO] Query marker FASTA was written to OceanDNA-b45554/markers.fasta
[2023-03-17 01:24:01,296] [INFO] Task started: Blastn
[2023-03-17 01:24:01,296] [INFO] Running command: blastn -query OceanDNA-b45554/markers.fasta -db /var/lib/cwl/stge74600f1-6e3f-4e4a-866f-25a06c5488af/dqc_reference/reference_markers.fasta -out OceanDNA-b45554/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:01,806] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:01,807] [INFO] Selected 11 target genomes.
[2023-03-17 01:24:01,807] [INFO] Target genome list was writen to OceanDNA-b45554/target_genomes.txt
[2023-03-17 01:24:01,814] [INFO] Task started: fastANI
[2023-03-17 01:24:01,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg9594123a-c35c-4379-ba80-b0c82817188c/OceanDNA-b45554.fa --refList OceanDNA-b45554/target_genomes.txt --output OceanDNA-b45554/fastani_result.tsv --threads 1
[2023-03-17 01:24:07,687] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:07,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge74600f1-6e3f-4e4a-866f-25a06c5488af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:24:07,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge74600f1-6e3f-4e4a-866f-25a06c5488af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:24:07,688] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:24:07,688] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 01:24:07,688] [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
--------------------------------------------------------------------------------
[2023-03-17 01:24:07,688] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45554/tc_result.tsv
[2023-03-17 01:24:07,688] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:24:07,689] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:24:07,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge74600f1-6e3f-4e4a-866f-25a06c5488af/dqc_reference/checkm_data
[2023-03-17 01:24:07,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:24:07,695] [INFO] Task started: CheckM
[2023-03-17 01:24:07,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45554/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45554/checkm_input OceanDNA-b45554/checkm_result
[2023-03-17 01:24:48,404] [INFO] Task succeeded: CheckM
[2023-03-17 01:24:48,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:24:48,406] [INFO] ===== Completeness check finished =====
[2023-03-17 01:24:48,406] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:24:48,406] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45554/markers.fasta)
[2023-03-17 01:24:48,407] [INFO] Task started: Blastn
[2023-03-17 01:24:48,407] [INFO] Running command: blastn -query OceanDNA-b45554/markers.fasta -db /var/lib/cwl/stge74600f1-6e3f-4e4a-866f-25a06c5488af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45554/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:49,088] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:49,089] [INFO] Selected 18 target genomes.
[2023-03-17 01:24:49,089] [INFO] Target genome list was writen to OceanDNA-b45554/target_genomes_gtdb.txt
[2023-03-17 01:24:49,647] [INFO] Task started: fastANI
[2023-03-17 01:24:49,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg9594123a-c35c-4379-ba80-b0c82817188c/OceanDNA-b45554.fa --refList OceanDNA-b45554/target_genomes_gtdb.txt --output OceanDNA-b45554/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:24:56,304] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:56,307] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 01:24:56,308] [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_018607205.1	s__MB11C04 sp018607205	99.0863	466	600	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.05	99.05	0.81	0.81	2	conclusive
GCA_018646565.1	s__MB11C04 sp018646565	86.0088	54	600	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686835.1	s__MB11C04 sp002686835	77.1358	133	600	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.34	99.34	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-17 01:24:56,308] [INFO] GTDB search result was written to OceanDNA-b45554/result_gtdb.tsv
[2023-03-17 01:24:56,308] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:24:56,308] [INFO] DFAST_QC result json was written to OceanDNA-b45554/dqc_result.json
[2023-03-17 01:24:56,308] [INFO] DFAST_QC completed!
[2023-03-17 01:24:56,309] [INFO] Total running time: 0h1m11s