[2023-03-19 02:16:59,733] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:16:59,733] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:16:59,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b323725-5fad-4376-a383-c196562ee563/dqc_reference
[2023-03-19 02:17:00,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:17:00,852] [INFO] Task started: Prodigal
[2023-03-19 02:17:00,852] [INFO] Running command: cat /var/lib/cwl/stg8fcaaa9e-320d-4097-a62c-42348aac1b5e/OceanDNA-b45576.fa | prodigal -d OceanDNA-b45576/cds.fna -a OceanDNA-b45576/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:17:15,294] [INFO] Task succeeded: Prodigal
[2023-03-19 02:17:15,294] [INFO] Task started: HMMsearch
[2023-03-19 02:17:15,294] [INFO] Running command: hmmsearch --tblout OceanDNA-b45576/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b323725-5fad-4376-a383-c196562ee563/dqc_reference/reference_markers.hmm OceanDNA-b45576/protein.faa > /dev/null
[2023-03-19 02:17:15,458] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:17:15,459] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8fcaaa9e-320d-4097-a62c-42348aac1b5e/OceanDNA-b45576.fa]
[2023-03-19 02:17:15,478] [INFO] Query marker FASTA was written to OceanDNA-b45576/markers.fasta
[2023-03-19 02:17:15,479] [INFO] Task started: Blastn
[2023-03-19 02:17:15,479] [INFO] Running command: blastn -query OceanDNA-b45576/markers.fasta -db /var/lib/cwl/stg5b323725-5fad-4376-a383-c196562ee563/dqc_reference/reference_markers.fasta -out OceanDNA-b45576/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:15,958] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:15,962] [INFO] Selected 5 target genomes.
[2023-03-19 02:17:15,962] [INFO] Target genome list was writen to OceanDNA-b45576/target_genomes.txt
[2023-03-19 02:17:15,965] [INFO] Task started: fastANI
[2023-03-19 02:17:15,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fcaaa9e-320d-4097-a62c-42348aac1b5e/OceanDNA-b45576.fa --refList OceanDNA-b45576/target_genomes.txt --output OceanDNA-b45576/fastani_result.tsv --threads 1
[2023-03-19 02:17:19,142] [INFO] Task succeeded: fastANI
[2023-03-19 02:17:19,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b323725-5fad-4376-a383-c196562ee563/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:17:19,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b323725-5fad-4376-a383-c196562ee563/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:17:19,143] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:17:19,143] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:17:19,143] [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
--------------------------------------------------------------------------------
[2023-03-19 02:17:19,143] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45576/tc_result.tsv
[2023-03-19 02:17:19,143] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:17:19,144] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:17:19,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b323725-5fad-4376-a383-c196562ee563/dqc_reference/checkm_data
[2023-03-19 02:17:19,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:17:19,150] [INFO] Task started: CheckM
[2023-03-19 02:17:19,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45576/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45576/checkm_input OceanDNA-b45576/checkm_result
[2023-03-19 02:18:00,819] [INFO] Task succeeded: CheckM
[2023-03-19 02:18:00,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:18:00,823] [INFO] ===== Completeness check finished =====
[2023-03-19 02:18:00,823] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:18:00,823] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45576/markers.fasta)
[2023-03-19 02:18:00,824] [INFO] Task started: Blastn
[2023-03-19 02:18:00,824] [INFO] Running command: blastn -query OceanDNA-b45576/markers.fasta -db /var/lib/cwl/stg5b323725-5fad-4376-a383-c196562ee563/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45576/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:18:01,556] [INFO] Task succeeded: Blastn
[2023-03-19 02:18:01,557] [INFO] Selected 16 target genomes.
[2023-03-19 02:18:01,557] [INFO] Target genome list was writen to OceanDNA-b45576/target_genomes_gtdb.txt
[2023-03-19 02:18:01,574] [INFO] Task started: fastANI
[2023-03-19 02:18:01,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fcaaa9e-320d-4097-a62c-42348aac1b5e/OceanDNA-b45576.fa --refList OceanDNA-b45576/target_genomes_gtdb.txt --output OceanDNA-b45576/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:18:08,456] [INFO] Task succeeded: fastANI
[2023-03-19 02:18:08,459] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:18:08,460] [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_018645725.1	s__MB11C04 sp018645725	82.7842	204	334	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500665.1	s__MB11C04 sp002500665	78.4673	116	334	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.37	95.55	0.93	0.84	7	-
GCA_002722545.1	s__MB11C04 sp002722545	77.7523	78	334	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:18:08,486] [INFO] GTDB search result was written to OceanDNA-b45576/result_gtdb.tsv
[2023-03-19 02:18:08,488] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:18:08,488] [INFO] DFAST_QC result json was written to OceanDNA-b45576/dqc_result.json
[2023-03-19 02:18:08,489] [INFO] DFAST_QC completed!
[2023-03-19 02:18:08,489] [INFO] Total running time: 0h1m9s