[2023-03-17 05:10:04,837] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:10:04,837] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:10:04,837] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb4f0da5-9738-4169-8b32-8c6cc02f0e3f/dqc_reference
[2023-03-17 05:10:06,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:10:06,045] [INFO] Task started: Prodigal
[2023-03-17 05:10:06,045] [INFO] Running command: cat /var/lib/cwl/stg0f87d445-3c6c-4e82-a70e-dbeba1644818/OceanDNA-b46644.fa | prodigal -d OceanDNA-b46644/cds.fna -a OceanDNA-b46644/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:10:26,002] [INFO] Task succeeded: Prodigal
[2023-03-17 05:10:26,003] [INFO] Task started: HMMsearch
[2023-03-17 05:10:26,003] [INFO] Running command: hmmsearch --tblout OceanDNA-b46644/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb4f0da5-9738-4169-8b32-8c6cc02f0e3f/dqc_reference/reference_markers.hmm OceanDNA-b46644/protein.faa > /dev/null
[2023-03-17 05:10:26,165] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:10:26,166] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0f87d445-3c6c-4e82-a70e-dbeba1644818/OceanDNA-b46644.fa]
[2023-03-17 05:10:26,181] [INFO] Query marker FASTA was written to OceanDNA-b46644/markers.fasta
[2023-03-17 05:10:26,182] [INFO] Task started: Blastn
[2023-03-17 05:10:26,182] [INFO] Running command: blastn -query OceanDNA-b46644/markers.fasta -db /var/lib/cwl/stgbb4f0da5-9738-4169-8b32-8c6cc02f0e3f/dqc_reference/reference_markers.fasta -out OceanDNA-b46644/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:26,669] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:26,670] [INFO] Selected 14 target genomes.
[2023-03-17 05:10:26,670] [INFO] Target genome list was writen to OceanDNA-b46644/target_genomes.txt
[2023-03-17 05:10:26,681] [INFO] Task started: fastANI
[2023-03-17 05:10:26,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f87d445-3c6c-4e82-a70e-dbeba1644818/OceanDNA-b46644.fa --refList OceanDNA-b46644/target_genomes.txt --output OceanDNA-b46644/fastani_result.tsv --threads 1
[2023-03-17 05:10:37,720] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:37,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb4f0da5-9738-4169-8b32-8c6cc02f0e3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:10:37,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb4f0da5-9738-4169-8b32-8c6cc02f0e3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:10:37,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:10:37,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:10:37,721] [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 05:10:37,722] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46644/tc_result.tsv
[2023-03-17 05:10:37,722] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:10:37,722] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:10:37,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb4f0da5-9738-4169-8b32-8c6cc02f0e3f/dqc_reference/checkm_data
[2023-03-17 05:10:37,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:10:37,788] [INFO] Task started: CheckM
[2023-03-17 05:10:37,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46644/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46644/checkm_input OceanDNA-b46644/checkm_result
[2023-03-17 05:11:30,059] [INFO] Task succeeded: CheckM
[2023-03-17 05:11:30,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 05:11:30,062] [INFO] ===== Completeness check finished =====
[2023-03-17 05:11:30,062] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:11:30,062] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46644/markers.fasta)
[2023-03-17 05:11:30,064] [INFO] Task started: Blastn
[2023-03-17 05:11:30,064] [INFO] Running command: blastn -query OceanDNA-b46644/markers.fasta -db /var/lib/cwl/stgbb4f0da5-9738-4169-8b32-8c6cc02f0e3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46644/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:11:30,706] [INFO] Task succeeded: Blastn
[2023-03-17 05:11:30,707] [INFO] Selected 16 target genomes.
[2023-03-17 05:11:30,707] [INFO] Target genome list was writen to OceanDNA-b46644/target_genomes_gtdb.txt
[2023-03-17 05:11:30,996] [INFO] Task started: fastANI
[2023-03-17 05:11:30,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f87d445-3c6c-4e82-a70e-dbeba1644818/OceanDNA-b46644.fa --refList OceanDNA-b46644/target_genomes_gtdb.txt --output OceanDNA-b46644/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:11:39,438] [INFO] Task succeeded: fastANI
[2023-03-17 05:11:39,441] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:11:39,441] [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_002724615.1	s__UBA6614 sp002724615	98.0781	382	638	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA6614	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002721895.1	s__UBA6614 sp002721895	80.3635	160	638	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA6614	95.0	97.45	95.11	0.88	0.86	3	-
GCA_002718935.1	s__UBA1100 sp002718935	78.8166	54	638	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:11:39,441] [INFO] GTDB search result was written to OceanDNA-b46644/result_gtdb.tsv
[2023-03-17 05:11:39,441] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:11:39,442] [INFO] DFAST_QC result json was written to OceanDNA-b46644/dqc_result.json
[2023-03-17 05:11:39,442] [INFO] DFAST_QC completed!
[2023-03-17 05:11:39,442] [INFO] Total running time: 0h1m35s