[2023-03-15 13:39:34,884] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:39:34,891] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:39:34,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d5c5fe2-5f22-4a21-8f3b-021ee4fabc74/dqc_reference
[2023-03-15 13:39:37,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:39:37,047] [INFO] Task started: Prodigal
[2023-03-15 13:39:37,047] [INFO] Running command: cat /var/lib/cwl/stgb1f61d82-7dde-4fb3-9fd7-61ef71e7b048/OceanDNA-b41689.fa | prodigal -d OceanDNA-b41689/cds.fna -a OceanDNA-b41689/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:39:42,154] [INFO] Task succeeded: Prodigal
[2023-03-15 13:39:42,154] [INFO] Task started: HMMsearch
[2023-03-15 13:39:42,154] [INFO] Running command: hmmsearch --tblout OceanDNA-b41689/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d5c5fe2-5f22-4a21-8f3b-021ee4fabc74/dqc_reference/reference_markers.hmm OceanDNA-b41689/protein.faa > /dev/null
[2023-03-15 13:39:42,337] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:39:42,338] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb1f61d82-7dde-4fb3-9fd7-61ef71e7b048/OceanDNA-b41689.fa]
[2023-03-15 13:39:42,408] [INFO] Query marker FASTA was written to OceanDNA-b41689/markers.fasta
[2023-03-15 13:39:42,409] [INFO] Task started: Blastn
[2023-03-15 13:39:42,409] [INFO] Running command: blastn -query OceanDNA-b41689/markers.fasta -db /var/lib/cwl/stg8d5c5fe2-5f22-4a21-8f3b-021ee4fabc74/dqc_reference/reference_markers.fasta -out OceanDNA-b41689/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:39:43,705] [INFO] Task succeeded: Blastn
[2023-03-15 13:39:43,729] [INFO] Selected 16 target genomes.
[2023-03-15 13:39:43,729] [INFO] Target genome list was writen to OceanDNA-b41689/target_genomes.txt
[2023-03-15 13:39:43,786] [INFO] Task started: fastANI
[2023-03-15 13:39:43,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f61d82-7dde-4fb3-9fd7-61ef71e7b048/OceanDNA-b41689.fa --refList OceanDNA-b41689/target_genomes.txt --output OceanDNA-b41689/fastani_result.tsv --threads 1
[2023-03-15 13:39:49,775] [INFO] Task succeeded: fastANI
[2023-03-15 13:39:49,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d5c5fe2-5f22-4a21-8f3b-021ee4fabc74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:39:49,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d5c5fe2-5f22-4a21-8f3b-021ee4fabc74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:39:49,776] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:39:49,776] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:39:49,776] [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
--------------------------------------------------------------------------------
[2023-03-15 13:39:49,783] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41689/tc_result.tsv
[2023-03-15 13:39:49,798] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:39:49,798] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:39:49,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d5c5fe2-5f22-4a21-8f3b-021ee4fabc74/dqc_reference/checkm_data
[2023-03-15 13:39:49,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:39:49,821] [INFO] Task started: CheckM
[2023-03-15 13:39:49,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41689/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41689/checkm_input OceanDNA-b41689/checkm_result
[2023-03-15 13:40:09,058] [INFO] Task succeeded: CheckM
[2023-03-15 13:40:09,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:40:09,162] [INFO] ===== Completeness check finished =====
[2023-03-15 13:40:09,163] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:40:09,163] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41689/markers.fasta)
[2023-03-15 13:40:09,163] [INFO] Task started: Blastn
[2023-03-15 13:40:09,163] [INFO] Running command: blastn -query OceanDNA-b41689/markers.fasta -db /var/lib/cwl/stg8d5c5fe2-5f22-4a21-8f3b-021ee4fabc74/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41689/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:40:09,982] [INFO] Task succeeded: Blastn
[2023-03-15 13:40:10,010] [INFO] Selected 7 target genomes.
[2023-03-15 13:40:10,010] [INFO] Target genome list was writen to OceanDNA-b41689/target_genomes_gtdb.txt
[2023-03-15 13:40:10,018] [INFO] Task started: fastANI
[2023-03-15 13:40:10,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f61d82-7dde-4fb3-9fd7-61ef71e7b048/OceanDNA-b41689.fa --refList OceanDNA-b41689/target_genomes_gtdb.txt --output OceanDNA-b41689/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:40:11,773] [INFO] Task succeeded: fastANI
[2023-03-15 13:40:11,777] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:40:11,778] [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_902578495.1	s__CACNYO01 sp902578495	92.448	272	321	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_902596665.1	s__CACNYO01 sp902596665	92.2902	294	321	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_902594855.1	s__CACNYO01 sp902594855	92.1662	282	321	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_902570035.1	s__CACNYO01 sp902570035	91.7443	267	321	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_902589965.1	s__CACNYO01 sp902589965	91.0656	244	321	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_902528485.1	s__CACNYO01 sp902528485	87.3853	175	321	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	86.5783	259	321	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	-
--------------------------------------------------------------------------------
[2023-03-15 13:40:11,788] [INFO] GTDB search result was written to OceanDNA-b41689/result_gtdb.tsv
[2023-03-15 13:40:11,807] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:40:11,817] [INFO] DFAST_QC result json was written to OceanDNA-b41689/dqc_result.json
[2023-03-15 13:40:11,817] [INFO] DFAST_QC completed!
[2023-03-15 13:40:11,817] [INFO] Total running time: 0h0m37s