[2023-03-18 08:36:16,006] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,006] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ab03beb-4b23-4593-be26-777587223f11/dqc_reference
[2023-03-18 08:36:17,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,826] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,826] [INFO] Running command: cat /var/lib/cwl/stge17d1ece-a7c6-4582-b465-86e13839b543/OceanDNA-b45131.fa | prodigal -d OceanDNA-b45131/cds.fna -a OceanDNA-b45131/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:34,805] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:34,806] [INFO] Task started: HMMsearch
[2023-03-18 08:36:34,806] [INFO] Running command: hmmsearch --tblout OceanDNA-b45131/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ab03beb-4b23-4593-be26-777587223f11/dqc_reference/reference_markers.hmm OceanDNA-b45131/protein.faa > /dev/null
[2023-03-18 08:36:35,047] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:35,048] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge17d1ece-a7c6-4582-b465-86e13839b543/OceanDNA-b45131.fa]
[2023-03-18 08:36:35,067] [INFO] Query marker FASTA was written to OceanDNA-b45131/markers.fasta
[2023-03-18 08:36:35,069] [INFO] Task started: Blastn
[2023-03-18 08:36:35,069] [INFO] Running command: blastn -query OceanDNA-b45131/markers.fasta -db /var/lib/cwl/stg2ab03beb-4b23-4593-be26-777587223f11/dqc_reference/reference_markers.fasta -out OceanDNA-b45131/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:35,587] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:35,588] [INFO] Selected 15 target genomes.
[2023-03-18 08:36:35,588] [INFO] Target genome list was writen to OceanDNA-b45131/target_genomes.txt
[2023-03-18 08:36:35,601] [INFO] Task started: fastANI
[2023-03-18 08:36:35,602] [INFO] Running command: fastANI --query /var/lib/cwl/stge17d1ece-a7c6-4582-b465-86e13839b543/OceanDNA-b45131.fa --refList OceanDNA-b45131/target_genomes.txt --output OceanDNA-b45131/fastani_result.tsv --threads 1
[2023-03-18 08:36:45,080] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:45,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ab03beb-4b23-4593-be26-777587223f11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:45,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ab03beb-4b23-4593-be26-777587223f11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:45,081] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:45,081] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:36:45,081] [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
--------------------------------------------------------------------------------
[2023-03-18 08:36:45,081] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45131/tc_result.tsv
[2023-03-18 08:36:45,081] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:45,081] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:45,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ab03beb-4b23-4593-be26-777587223f11/dqc_reference/checkm_data
[2023-03-18 08:36:45,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:45,089] [INFO] Task started: CheckM
[2023-03-18 08:36:45,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45131/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45131/checkm_input OceanDNA-b45131/checkm_result
[2023-03-18 08:37:23,183] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:23,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:23,188] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:23,188] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:23,188] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45131/markers.fasta)
[2023-03-18 08:37:23,189] [INFO] Task started: Blastn
[2023-03-18 08:37:23,189] [INFO] Running command: blastn -query OceanDNA-b45131/markers.fasta -db /var/lib/cwl/stg2ab03beb-4b23-4593-be26-777587223f11/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45131/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:23,953] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:23,955] [INFO] Selected 29 target genomes.
[2023-03-18 08:37:23,955] [INFO] Target genome list was writen to OceanDNA-b45131/target_genomes_gtdb.txt
[2023-03-18 08:37:23,994] [INFO] Task started: fastANI
[2023-03-18 08:37:23,994] [INFO] Running command: fastANI --query /var/lib/cwl/stge17d1ece-a7c6-4582-b465-86e13839b543/OceanDNA-b45131.fa --refList OceanDNA-b45131/target_genomes_gtdb.txt --output OceanDNA-b45131/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:39,804] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:39,806] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:37:39,807] [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_001469005.2	s__UBA1014 sp001469005	95.0	371	413	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__UBA1014	95.0	97.51	95.82	0.84	0.66	8	-
GCA_002683785.1	s__UBA1014 sp002683785	78.5314	172	413	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__UBA1014	95.0	99.25	99.16	0.82	0.74	8	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:39,808] [INFO] GTDB search result was written to OceanDNA-b45131/result_gtdb.tsv
[2023-03-18 08:37:39,810] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:39,812] [INFO] DFAST_QC result json was written to OceanDNA-b45131/dqc_result.json
[2023-03-18 08:37:39,812] [INFO] DFAST_QC completed!
[2023-03-18 08:37:39,812] [INFO] Total running time: 0h1m24s