[2023-03-16 06:12:34,967] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:12:34,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:12:34,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg671fca6b-cc80-4ba6-95fe-1cd50f616442/dqc_reference
[2023-03-16 06:12:36,627] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:12:36,627] [INFO] Task started: Prodigal
[2023-03-16 06:12:36,627] [INFO] Running command: cat /var/lib/cwl/stg8c283926-9fc6-494c-bd8a-a8351a95604f/OceanDNA-b31172.fa | prodigal -d OceanDNA-b31172/cds.fna -a OceanDNA-b31172/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:13:01,977] [INFO] Task succeeded: Prodigal
[2023-03-16 06:13:01,977] [INFO] Task started: HMMsearch
[2023-03-16 06:13:01,977] [INFO] Running command: hmmsearch --tblout OceanDNA-b31172/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg671fca6b-cc80-4ba6-95fe-1cd50f616442/dqc_reference/reference_markers.hmm OceanDNA-b31172/protein.faa > /dev/null
[2023-03-16 06:13:02,209] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:13:02,209] [INFO] Found 6/6 markers.
[2023-03-16 06:13:02,245] [INFO] Query marker FASTA was written to OceanDNA-b31172/markers.fasta
[2023-03-16 06:13:02,247] [INFO] Task started: Blastn
[2023-03-16 06:13:02,247] [INFO] Running command: blastn -query OceanDNA-b31172/markers.fasta -db /var/lib/cwl/stg671fca6b-cc80-4ba6-95fe-1cd50f616442/dqc_reference/reference_markers.fasta -out OceanDNA-b31172/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:02,890] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:02,895] [INFO] Selected 32 target genomes.
[2023-03-16 06:13:02,895] [INFO] Target genome list was writen to OceanDNA-b31172/target_genomes.txt
[2023-03-16 06:13:02,940] [INFO] Task started: fastANI
[2023-03-16 06:13:02,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c283926-9fc6-494c-bd8a-a8351a95604f/OceanDNA-b31172.fa --refList OceanDNA-b31172/target_genomes.txt --output OceanDNA-b31172/fastani_result.tsv --threads 1
[2023-03-16 06:13:27,208] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:27,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg671fca6b-cc80-4ba6-95fe-1cd50f616442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:13:27,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg671fca6b-cc80-4ba6-95fe-1cd50f616442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:13:27,209] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:13:27,209] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:13:27,209] [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 06:13:27,212] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31172/tc_result.tsv
[2023-03-16 06:13:27,217] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:13:27,217] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:13:27,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg671fca6b-cc80-4ba6-95fe-1cd50f616442/dqc_reference/checkm_data
[2023-03-16 06:13:27,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:13:27,232] [INFO] Task started: CheckM
[2023-03-16 06:13:27,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31172/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31172/checkm_input OceanDNA-b31172/checkm_result
[2023-03-16 06:14:29,172] [INFO] Task succeeded: CheckM
[2023-03-16 06:14:29,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:14:29,199] [INFO] ===== Completeness check finished =====
[2023-03-16 06:14:29,200] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:14:29,200] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31172/markers.fasta)
[2023-03-16 06:14:29,201] [INFO] Task started: Blastn
[2023-03-16 06:14:29,201] [INFO] Running command: blastn -query OceanDNA-b31172/markers.fasta -db /var/lib/cwl/stg671fca6b-cc80-4ba6-95fe-1cd50f616442/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31172/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:14:30,311] [INFO] Task succeeded: Blastn
[2023-03-16 06:14:30,319] [INFO] Selected 22 target genomes.
[2023-03-16 06:14:30,319] [INFO] Target genome list was writen to OceanDNA-b31172/target_genomes_gtdb.txt
[2023-03-16 06:14:30,356] [INFO] Task started: fastANI
[2023-03-16 06:14:30,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c283926-9fc6-494c-bd8a-a8351a95604f/OceanDNA-b31172.fa --refList OceanDNA-b31172/target_genomes_gtdb.txt --output OceanDNA-b31172/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:14:44,351] [INFO] Task succeeded: fastANI
[2023-03-16 06:14:44,357] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:14:44,357] [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_002327565.1	s__UBA2165 sp002327565	99.8599	1226	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__UBA2165	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018649245.1	s__UBA2165 sp018649245	82.6496	624	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__UBA2165	95.0	99.23	99.23	0.84	0.84	2	-
GCA_018649725.1	s__TMED23 sp018649725	78.0922	437	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__TMED23	95.0	99.78	99.75	0.87	0.87	3	-
GCA_002725625.1	s__GCA-2725625 sp002725625	76.8111	119	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2725625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687515.1	s__GCA-2687515 sp002687515	76.6534	130	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2687515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960465.1	s__TMED23 sp012960465	76.3476	63	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__TMED23	95.0	99.66	99.66	0.84	0.84	2	-
GCA_018674495.1	s__GCA-2687515 sp018674495	76.1985	90	1371	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2687515	95.0	99.77	99.72	0.95	0.94	13	-
--------------------------------------------------------------------------------
[2023-03-16 06:14:44,360] [INFO] GTDB search result was written to OceanDNA-b31172/result_gtdb.tsv
[2023-03-16 06:14:44,368] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:14:44,375] [INFO] DFAST_QC result json was written to OceanDNA-b31172/dqc_result.json
[2023-03-16 06:14:44,375] [INFO] DFAST_QC completed!
[2023-03-16 06:14:44,375] [INFO] Total running time: 0h2m9s