[2023-03-16 04:54:07,031] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,032] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,032] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb1e1278-2c29-48cd-860b-5af705cd7c69/dqc_reference
[2023-03-16 04:54:08,342] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,342] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,342] [INFO] Running command: cat /var/lib/cwl/stg4716e735-3faa-4efb-8de1-dfdf1bbf833f/OceanDNA-b41620.fa | prodigal -d OceanDNA-b41620/cds.fna -a OceanDNA-b41620/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:19,086] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:19,086] [INFO] Task started: HMMsearch
[2023-03-16 04:54:19,086] [INFO] Running command: hmmsearch --tblout OceanDNA-b41620/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb1e1278-2c29-48cd-860b-5af705cd7c69/dqc_reference/reference_markers.hmm OceanDNA-b41620/protein.faa > /dev/null
[2023-03-16 04:54:19,284] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:19,285] [INFO] Found 6/6 markers.
[2023-03-16 04:54:19,298] [INFO] Query marker FASTA was written to OceanDNA-b41620/markers.fasta
[2023-03-16 04:54:19,299] [INFO] Task started: Blastn
[2023-03-16 04:54:19,299] [INFO] Running command: blastn -query OceanDNA-b41620/markers.fasta -db /var/lib/cwl/stgcb1e1278-2c29-48cd-860b-5af705cd7c69/dqc_reference/reference_markers.fasta -out OceanDNA-b41620/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:19,891] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:19,892] [INFO] Selected 35 target genomes.
[2023-03-16 04:54:19,892] [INFO] Target genome list was writen to OceanDNA-b41620/target_genomes.txt
[2023-03-16 04:54:19,909] [INFO] Task started: fastANI
[2023-03-16 04:54:19,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg4716e735-3faa-4efb-8de1-dfdf1bbf833f/OceanDNA-b41620.fa --refList OceanDNA-b41620/target_genomes.txt --output OceanDNA-b41620/fastani_result.tsv --threads 1
[2023-03-16 04:54:40,691] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:40,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb1e1278-2c29-48cd-860b-5af705cd7c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:40,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb1e1278-2c29-48cd-860b-5af705cd7c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:40,692] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:40,692] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:40,692] [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 04:54:40,693] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41620/tc_result.tsv
[2023-03-16 04:54:40,706] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:40,706] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:40,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb1e1278-2c29-48cd-860b-5af705cd7c69/dqc_reference/checkm_data
[2023-03-16 04:54:40,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:40,762] [INFO] Task started: CheckM
[2023-03-16 04:54:40,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41620/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41620/checkm_input OceanDNA-b41620/checkm_result
[2023-03-16 04:55:13,944] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:13,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:13,947] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:13,947] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:13,947] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41620/markers.fasta)
[2023-03-16 04:55:13,947] [INFO] Task started: Blastn
[2023-03-16 04:55:13,947] [INFO] Running command: blastn -query OceanDNA-b41620/markers.fasta -db /var/lib/cwl/stgcb1e1278-2c29-48cd-860b-5af705cd7c69/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41620/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:14,896] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:14,898] [INFO] Selected 25 target genomes.
[2023-03-16 04:55:14,898] [INFO] Target genome list was writen to OceanDNA-b41620/target_genomes_gtdb.txt
[2023-03-16 04:55:14,927] [INFO] Task started: fastANI
[2023-03-16 04:55:14,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg4716e735-3faa-4efb-8de1-dfdf1bbf833f/OceanDNA-b41620.fa --refList OceanDNA-b41620/target_genomes_gtdb.txt --output OceanDNA-b41620/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:27,653] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:27,657] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:55:27,658] [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_002339085.1	s__UBA7434 sp002339085	99.83	581	653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.78	99.78	0.84	0.84	2	conclusive
GCA_002726445.1	s__UBA7434 sp002726445	88.6245	351	653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.17	99.17	0.72	0.72	2	-
GCA_002336035.1	s__UBA7434 sp002336035	78.6622	276	653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018668095.1	s__UBA7434 sp018668095	77.3606	57	653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	98.20	98.20	0.79	0.79	2	-
GCA_905480475.1	s__UBA7434 sp905480475	76.3548	60	653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:27,658] [INFO] GTDB search result was written to OceanDNA-b41620/result_gtdb.tsv
[2023-03-16 04:55:27,658] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:27,659] [INFO] DFAST_QC result json was written to OceanDNA-b41620/dqc_result.json
[2023-03-16 04:55:27,659] [INFO] DFAST_QC completed!
[2023-03-16 04:55:27,659] [INFO] Total running time: 0h1m21s