[2023-03-17 09:05:02,613] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,614] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg599bdc07-be1a-4ba9-a16a-3eea0d77317c/dqc_reference
[2023-03-17 09:05:03,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,813] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,814] [INFO] Running command: cat /var/lib/cwl/stg46fa0ea8-6cf5-4b2f-891c-d796e68183df/OceanDNA-b24707.fa | prodigal -d OceanDNA-b24707/cds.fna -a OceanDNA-b24707/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:17,502] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:17,502] [INFO] Task started: HMMsearch
[2023-03-17 09:05:17,502] [INFO] Running command: hmmsearch --tblout OceanDNA-b24707/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg599bdc07-be1a-4ba9-a16a-3eea0d77317c/dqc_reference/reference_markers.hmm OceanDNA-b24707/protein.faa > /dev/null
[2023-03-17 09:05:17,677] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:17,677] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg46fa0ea8-6cf5-4b2f-891c-d796e68183df/OceanDNA-b24707.fa]
[2023-03-17 09:05:17,692] [INFO] Query marker FASTA was written to OceanDNA-b24707/markers.fasta
[2023-03-17 09:05:17,693] [INFO] Task started: Blastn
[2023-03-17 09:05:17,693] [INFO] Running command: blastn -query OceanDNA-b24707/markers.fasta -db /var/lib/cwl/stg599bdc07-be1a-4ba9-a16a-3eea0d77317c/dqc_reference/reference_markers.fasta -out OceanDNA-b24707/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:18,340] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:18,340] [INFO] Selected 29 target genomes.
[2023-03-17 09:05:18,341] [INFO] Target genome list was writen to OceanDNA-b24707/target_genomes.txt
[2023-03-17 09:05:18,441] [INFO] Task started: fastANI
[2023-03-17 09:05:18,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg46fa0ea8-6cf5-4b2f-891c-d796e68183df/OceanDNA-b24707.fa --refList OceanDNA-b24707/target_genomes.txt --output OceanDNA-b24707/fastani_result.tsv --threads 1
[2023-03-17 09:05:39,308] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:39,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg599bdc07-be1a-4ba9-a16a-3eea0d77317c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:39,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg599bdc07-be1a-4ba9-a16a-3eea0d77317c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:39,308] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:39,309] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:05:39,309] [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 09:05:39,309] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24707/tc_result.tsv
[2023-03-17 09:05:39,309] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:39,309] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:39,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg599bdc07-be1a-4ba9-a16a-3eea0d77317c/dqc_reference/checkm_data
[2023-03-17 09:05:39,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:39,383] [INFO] Task started: CheckM
[2023-03-17 09:05:39,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24707/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24707/checkm_input OceanDNA-b24707/checkm_result
[2023-03-17 09:06:16,284] [INFO] Task succeeded: CheckM
[2023-03-17 09:06:16,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:06:16,287] [INFO] ===== Completeness check finished =====
[2023-03-17 09:06:16,287] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:06:16,287] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24707/markers.fasta)
[2023-03-17 09:06:16,289] [INFO] Task started: Blastn
[2023-03-17 09:06:16,289] [INFO] Running command: blastn -query OceanDNA-b24707/markers.fasta -db /var/lib/cwl/stg599bdc07-be1a-4ba9-a16a-3eea0d77317c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24707/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:06:17,418] [INFO] Task succeeded: Blastn
[2023-03-17 09:06:17,419] [INFO] Selected 14 target genomes.
[2023-03-17 09:06:17,419] [INFO] Target genome list was writen to OceanDNA-b24707/target_genomes_gtdb.txt
[2023-03-17 09:06:17,551] [INFO] Task started: fastANI
[2023-03-17 09:06:17,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg46fa0ea8-6cf5-4b2f-891c-d796e68183df/OceanDNA-b24707.fa --refList OceanDNA-b24707/target_genomes_gtdb.txt --output OceanDNA-b24707/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:06:25,609] [INFO] Task succeeded: fastANI
[2023-03-17 09:06:25,612] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:06:25,612] [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_013285465.1	s__CSBR16-224 sp013285465	97.5718	694	723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__CSBR16-224	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_006226225.1	s__CSBR16-224 sp006226225	86.8017	484	723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__CSBR16-224	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007116755.1	s__CSBR16-224 sp007116755	78.6126	251	723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__CSBR16-224	95.0	95.68	95.68	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:06:25,613] [INFO] GTDB search result was written to OceanDNA-b24707/result_gtdb.tsv
[2023-03-17 09:06:25,613] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:06:25,613] [INFO] DFAST_QC result json was written to OceanDNA-b24707/dqc_result.json
[2023-03-17 09:06:25,613] [INFO] DFAST_QC completed!
[2023-03-17 09:06:25,613] [INFO] Total running time: 0h1m23s