[2023-03-16 10:46:24,047] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:46:24,047] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:46:24,047] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6cf7f99-bb01-4b49-9d66-c25cb5c4192a/dqc_reference
[2023-03-16 10:46:25,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:46:25,193] [INFO] Task started: Prodigal
[2023-03-16 10:46:25,193] [INFO] Running command: cat /var/lib/cwl/stg68c9b6ac-eb19-49de-951b-6d6cf5ee85d5/OceanDNA-b45348.fa | prodigal -d OceanDNA-b45348/cds.fna -a OceanDNA-b45348/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:46:32,220] [INFO] Task succeeded: Prodigal
[2023-03-16 10:46:32,220] [INFO] Task started: HMMsearch
[2023-03-16 10:46:32,220] [INFO] Running command: hmmsearch --tblout OceanDNA-b45348/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6cf7f99-bb01-4b49-9d66-c25cb5c4192a/dqc_reference/reference_markers.hmm OceanDNA-b45348/protein.faa > /dev/null
[2023-03-16 10:46:32,416] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:46:32,416] [INFO] Found 6/6 markers.
[2023-03-16 10:46:32,425] [INFO] Query marker FASTA was written to OceanDNA-b45348/markers.fasta
[2023-03-16 10:46:32,427] [INFO] Task started: Blastn
[2023-03-16 10:46:32,427] [INFO] Running command: blastn -query OceanDNA-b45348/markers.fasta -db /var/lib/cwl/stgf6cf7f99-bb01-4b49-9d66-c25cb5c4192a/dqc_reference/reference_markers.fasta -out OceanDNA-b45348/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:46:33,131] [INFO] Task succeeded: Blastn
[2023-03-16 10:46:33,132] [INFO] Selected 14 target genomes.
[2023-03-16 10:46:33,132] [INFO] Target genome list was writen to OceanDNA-b45348/target_genomes.txt
[2023-03-16 10:46:33,187] [INFO] Task started: fastANI
[2023-03-16 10:46:33,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c9b6ac-eb19-49de-951b-6d6cf5ee85d5/OceanDNA-b45348.fa --refList OceanDNA-b45348/target_genomes.txt --output OceanDNA-b45348/fastani_result.tsv --threads 1
[2023-03-16 10:46:39,889] [INFO] Task succeeded: fastANI
[2023-03-16 10:46:39,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6cf7f99-bb01-4b49-9d66-c25cb5c4192a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:46:39,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6cf7f99-bb01-4b49-9d66-c25cb5c4192a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:46:39,890] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:46:39,890] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:46:39,890] [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 10:46:39,890] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45348/tc_result.tsv
[2023-03-16 10:46:39,891] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:46:39,891] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:46:39,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6cf7f99-bb01-4b49-9d66-c25cb5c4192a/dqc_reference/checkm_data
[2023-03-16 10:46:39,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:46:39,947] [INFO] Task started: CheckM
[2023-03-16 10:46:39,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45348/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45348/checkm_input OceanDNA-b45348/checkm_result
[2023-03-16 10:47:15,049] [INFO] Task succeeded: CheckM
[2023-03-16 10:47:15,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:47:15,051] [INFO] ===== Completeness check finished =====
[2023-03-16 10:47:15,051] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:47:15,051] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45348/markers.fasta)
[2023-03-16 10:47:15,053] [INFO] Task started: Blastn
[2023-03-16 10:47:15,053] [INFO] Running command: blastn -query OceanDNA-b45348/markers.fasta -db /var/lib/cwl/stgf6cf7f99-bb01-4b49-9d66-c25cb5c4192a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45348/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:47:16,619] [INFO] Task succeeded: Blastn
[2023-03-16 10:47:16,620] [INFO] Selected 20 target genomes.
[2023-03-16 10:47:16,620] [INFO] Target genome list was writen to OceanDNA-b45348/target_genomes_gtdb.txt
[2023-03-16 10:47:16,667] [INFO] Task started: fastANI
[2023-03-16 10:47:16,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c9b6ac-eb19-49de-951b-6d6cf5ee85d5/OceanDNA-b45348.fa --refList OceanDNA-b45348/target_genomes_gtdb.txt --output OceanDNA-b45348/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:47:25,593] [INFO] Task succeeded: fastANI
[2023-03-16 10:47:25,596] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:47:25,596] [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_003532555.1	s__UBA1859 sp003532555	98.4634	246	411	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA1859	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002338345.1	s__UBA1859 sp002338345	84.6275	199	411	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA1859	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691095.1	s__UBA1859 sp002691095	78.1986	106	411	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA1859	95.0	98.96	98.96	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-16 10:47:25,597] [INFO] GTDB search result was written to OceanDNA-b45348/result_gtdb.tsv
[2023-03-16 10:47:25,597] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:47:25,597] [INFO] DFAST_QC result json was written to OceanDNA-b45348/dqc_result.json
[2023-03-16 10:47:25,597] [INFO] DFAST_QC completed!
[2023-03-16 10:47:25,597] [INFO] Total running time: 0h1m2s