[2023-03-16 16:35:56,424] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:35:56,424] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:35:56,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg92e01046-5775-4476-a14d-d6cd0451793f/dqc_reference
[2023-03-16 16:35:57,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:35:57,560] [INFO] Task started: Prodigal
[2023-03-16 16:35:57,561] [INFO] Running command: cat /var/lib/cwl/stgb63b7fc8-c4fa-42d8-9f5c-56707a373f96/OceanDNA-b5446.fa | prodigal -d OceanDNA-b5446/cds.fna -a OceanDNA-b5446/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:36:18,501] [INFO] Task succeeded: Prodigal
[2023-03-16 16:36:18,501] [INFO] Task started: HMMsearch
[2023-03-16 16:36:18,502] [INFO] Running command: hmmsearch --tblout OceanDNA-b5446/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92e01046-5775-4476-a14d-d6cd0451793f/dqc_reference/reference_markers.hmm OceanDNA-b5446/protein.faa > /dev/null
[2023-03-16 16:36:18,875] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:36:18,875] [INFO] Found 6/6 markers.
[2023-03-16 16:36:18,890] [INFO] Query marker FASTA was written to OceanDNA-b5446/markers.fasta
[2023-03-16 16:36:18,895] [INFO] Task started: Blastn
[2023-03-16 16:36:18,895] [INFO] Running command: blastn -query OceanDNA-b5446/markers.fasta -db /var/lib/cwl/stg92e01046-5775-4476-a14d-d6cd0451793f/dqc_reference/reference_markers.fasta -out OceanDNA-b5446/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:36:20,024] [INFO] Task succeeded: Blastn
[2023-03-16 16:36:20,025] [INFO] Selected 29 target genomes.
[2023-03-16 16:36:20,025] [INFO] Target genome list was writen to OceanDNA-b5446/target_genomes.txt
[2023-03-16 16:36:20,055] [INFO] Task started: fastANI
[2023-03-16 16:36:20,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgb63b7fc8-c4fa-42d8-9f5c-56707a373f96/OceanDNA-b5446.fa --refList OceanDNA-b5446/target_genomes.txt --output OceanDNA-b5446/fastani_result.tsv --threads 1
[2023-03-16 16:36:38,993] [INFO] Task succeeded: fastANI
[2023-03-16 16:36:38,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92e01046-5775-4476-a14d-d6cd0451793f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:36:38,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92e01046-5775-4476-a14d-d6cd0451793f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:36:38,994] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:36:38,994] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:36:38,994] [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 16:36:38,994] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5446/tc_result.tsv
[2023-03-16 16:36:38,994] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:36:38,994] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:36:38,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92e01046-5775-4476-a14d-d6cd0451793f/dqc_reference/checkm_data
[2023-03-16 16:36:38,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:36:39,001] [INFO] Task started: CheckM
[2023-03-16 16:36:39,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5446/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5446/checkm_input OceanDNA-b5446/checkm_result
[2023-03-16 16:37:18,549] [INFO] Task succeeded: CheckM
[2023-03-16 16:37:18,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:37:18,552] [INFO] ===== Completeness check finished =====
[2023-03-16 16:37:18,552] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:37:18,552] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5446/markers.fasta)
[2023-03-16 16:37:18,553] [INFO] Task started: Blastn
[2023-03-16 16:37:18,553] [INFO] Running command: blastn -query OceanDNA-b5446/markers.fasta -db /var/lib/cwl/stg92e01046-5775-4476-a14d-d6cd0451793f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5446/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:37:19,240] [INFO] Task succeeded: Blastn
[2023-03-16 16:37:19,241] [INFO] Selected 33 target genomes.
[2023-03-16 16:37:19,241] [INFO] Target genome list was writen to OceanDNA-b5446/target_genomes_gtdb.txt
[2023-03-16 16:37:19,635] [INFO] Task started: fastANI
[2023-03-16 16:37:19,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgb63b7fc8-c4fa-42d8-9f5c-56707a373f96/OceanDNA-b5446.fa --refList OceanDNA-b5446/target_genomes_gtdb.txt --output OceanDNA-b5446/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:37:35,174] [INFO] Task succeeded: fastANI
[2023-03-16 16:37:35,178] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:37:35,178] [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_002167775.1	s__UBA952 sp002167775	79.436	277	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.23	98.23	0.91	0.91	2	-
GCA_002480215.1	s__UBA952 sp002480215	79.2407	234	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.70	99.70	0.81	0.81	2	-
GCA_002683585.1	s__UBA952 sp002683585	78.4217	146	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182775.1	s__UBA952 sp905182775	77.7464	164	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665005.1	s__UBA952 sp018665005	76.9053	99	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.77	98.77	0.77	0.77	2	-
GCA_905480165.1	s__UBA952 sp905480165	76.8628	77	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:37:35,179] [INFO] GTDB search result was written to OceanDNA-b5446/result_gtdb.tsv
[2023-03-16 16:37:35,179] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:37:35,179] [INFO] DFAST_QC result json was written to OceanDNA-b5446/dqc_result.json
[2023-03-16 16:37:35,180] [INFO] DFAST_QC completed!
[2023-03-16 16:37:35,180] [INFO] Total running time: 0h1m39s