[2023-03-17 23:09:11,912] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:09:11,913] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:09:11,913] [INFO] DQC Reference Directory: /var/lib/cwl/stg50c7abc5-047d-4abb-8027-29766059ac82/dqc_reference
[2023-03-17 23:09:13,007] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:09:13,007] [INFO] Task started: Prodigal
[2023-03-17 23:09:13,007] [INFO] Running command: cat /var/lib/cwl/stge8e4ba88-4b88-4ec0-b7c4-daf57b446c56/OceanDNA-b41690.fa | prodigal -d OceanDNA-b41690/cds.fna -a OceanDNA-b41690/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:09:17,334] [INFO] Task succeeded: Prodigal
[2023-03-17 23:09:17,335] [INFO] Task started: HMMsearch
[2023-03-17 23:09:17,335] [INFO] Running command: hmmsearch --tblout OceanDNA-b41690/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50c7abc5-047d-4abb-8027-29766059ac82/dqc_reference/reference_markers.hmm OceanDNA-b41690/protein.faa > /dev/null
[2023-03-17 23:09:17,503] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:09:17,503] [INFO] Found 6/6 markers.
[2023-03-17 23:09:17,521] [INFO] Query marker FASTA was written to OceanDNA-b41690/markers.fasta
[2023-03-17 23:09:17,522] [INFO] Task started: Blastn
[2023-03-17 23:09:17,523] [INFO] Running command: blastn -query OceanDNA-b41690/markers.fasta -db /var/lib/cwl/stg50c7abc5-047d-4abb-8027-29766059ac82/dqc_reference/reference_markers.fasta -out OceanDNA-b41690/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:18,014] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:18,019] [INFO] Selected 8 target genomes.
[2023-03-17 23:09:18,019] [INFO] Target genome list was writen to OceanDNA-b41690/target_genomes.txt
[2023-03-17 23:09:18,023] [INFO] Task started: fastANI
[2023-03-17 23:09:18,023] [INFO] Running command: fastANI --query /var/lib/cwl/stge8e4ba88-4b88-4ec0-b7c4-daf57b446c56/OceanDNA-b41690.fa --refList OceanDNA-b41690/target_genomes.txt --output OceanDNA-b41690/fastani_result.tsv --threads 1
[2023-03-17 23:09:22,292] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:22,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50c7abc5-047d-4abb-8027-29766059ac82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:22,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50c7abc5-047d-4abb-8027-29766059ac82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:22,293] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:22,293] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:09:22,293] [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 23:09:22,295] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41690/tc_result.tsv
[2023-03-17 23:09:22,297] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:22,297] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:22,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50c7abc5-047d-4abb-8027-29766059ac82/dqc_reference/checkm_data
[2023-03-17 23:09:22,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:22,305] [INFO] Task started: CheckM
[2023-03-17 23:09:22,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41690/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41690/checkm_input OceanDNA-b41690/checkm_result
[2023-03-17 23:09:38,230] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:38,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.14%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 23:09:38,258] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:38,259] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:38,259] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41690/markers.fasta)
[2023-03-17 23:09:38,259] [INFO] Task started: Blastn
[2023-03-17 23:09:38,259] [INFO] Running command: blastn -query OceanDNA-b41690/markers.fasta -db /var/lib/cwl/stg50c7abc5-047d-4abb-8027-29766059ac82/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41690/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:38,928] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:38,931] [INFO] Selected 10 target genomes.
[2023-03-17 23:09:38,931] [INFO] Target genome list was writen to OceanDNA-b41690/target_genomes_gtdb.txt
[2023-03-17 23:09:38,942] [INFO] Task started: fastANI
[2023-03-17 23:09:38,942] [INFO] Running command: fastANI --query /var/lib/cwl/stge8e4ba88-4b88-4ec0-b7c4-daf57b446c56/OceanDNA-b41690.fa --refList OceanDNA-b41690/target_genomes_gtdb.txt --output OceanDNA-b41690/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:09:40,914] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:40,919] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:09:40,920] [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_902624765.1	s__CACNYO01 sp902624765	95.4493	102	154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902596665.1	s__CACNYO01 sp902596665	88.6383	141	154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	95.60	95.38	0.89	0.88	7	-
GCA_902578495.1	s__CACNYO01 sp902578495	88.107	137	154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589965.1	s__CACNYO01 sp902589965	87.7618	119	154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	95.54	95.01	0.78	0.76	10	-
GCA_902570035.1	s__CACNYO01 sp902570035	87.4991	126	154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	96.39	95.41	0.82	0.78	11	-
GCA_902594855.1	s__CACNYO01 sp902594855	87.4601	140	154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	96.60	95.51	0.88	0.82	11	-
GCA_902528485.1	s__CACNYO01 sp902528485	86.1901	84	154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	95.61	95.61	0.68	0.68	2	-
GCA_902526045.1	s__CACNYO01 sp902526045	85.6089	128	154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:09:40,921] [INFO] GTDB search result was written to OceanDNA-b41690/result_gtdb.tsv
[2023-03-17 23:09:40,921] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:09:40,924] [INFO] DFAST_QC result json was written to OceanDNA-b41690/dqc_result.json
[2023-03-17 23:09:40,924] [INFO] DFAST_QC completed!
[2023-03-17 23:09:40,924] [INFO] Total running time: 0h0m29s