[2023-03-15 05:29:12,506] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:12,507] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:12,507] [INFO] DQC Reference Directory: /var/lib/cwl/stgbebec796-4689-4248-bf01-c47ffbccdddd/dqc_reference
[2023-03-15 05:29:13,615] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:13,615] [INFO] Task started: Prodigal
[2023-03-15 05:29:13,615] [INFO] Running command: cat /var/lib/cwl/stg1ac5289a-de52-40ee-9c9c-d5e55902fbb5/OceanDNA-b12614.fa | prodigal -d OceanDNA-b12614/cds.fna -a OceanDNA-b12614/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:29,068] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:29,068] [INFO] Task started: HMMsearch
[2023-03-15 05:29:29,069] [INFO] Running command: hmmsearch --tblout OceanDNA-b12614/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbebec796-4689-4248-bf01-c47ffbccdddd/dqc_reference/reference_markers.hmm OceanDNA-b12614/protein.faa > /dev/null
[2023-03-15 05:29:29,305] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:29,305] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1ac5289a-de52-40ee-9c9c-d5e55902fbb5/OceanDNA-b12614.fa]
[2023-03-15 05:29:29,324] [INFO] Query marker FASTA was written to OceanDNA-b12614/markers.fasta
[2023-03-15 05:29:29,324] [INFO] Task started: Blastn
[2023-03-15 05:29:29,324] [INFO] Running command: blastn -query OceanDNA-b12614/markers.fasta -db /var/lib/cwl/stgbebec796-4689-4248-bf01-c47ffbccdddd/dqc_reference/reference_markers.fasta -out OceanDNA-b12614/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:29,898] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:29,899] [INFO] Selected 34 target genomes.
[2023-03-15 05:29:29,899] [INFO] Target genome list was writen to OceanDNA-b12614/target_genomes.txt
[2023-03-15 05:29:29,916] [INFO] Task started: fastANI
[2023-03-15 05:29:29,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac5289a-de52-40ee-9c9c-d5e55902fbb5/OceanDNA-b12614.fa --refList OceanDNA-b12614/target_genomes.txt --output OceanDNA-b12614/fastani_result.tsv --threads 1
[2023-03-15 05:29:50,283] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:50,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbebec796-4689-4248-bf01-c47ffbccdddd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:50,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbebec796-4689-4248-bf01-c47ffbccdddd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:50,286] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:50,286] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:50,286] [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
Vicingus serpentipes	strain=NCIMB 15042	GCA_007993035.1	1926625	1926625	type	True	76.4845	127	770	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:50,286] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12614/tc_result.tsv
[2023-03-15 05:29:50,286] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:50,286] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:50,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbebec796-4689-4248-bf01-c47ffbccdddd/dqc_reference/checkm_data
[2023-03-15 05:29:50,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:50,291] [INFO] Task started: CheckM
[2023-03-15 05:29:50,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12614/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12614/checkm_input OceanDNA-b12614/checkm_result
[2023-03-15 05:30:30,727] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:30,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:30,730] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:30,730] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:30,730] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12614/markers.fasta)
[2023-03-15 05:30:30,730] [INFO] Task started: Blastn
[2023-03-15 05:30:30,730] [INFO] Running command: blastn -query OceanDNA-b12614/markers.fasta -db /var/lib/cwl/stgbebec796-4689-4248-bf01-c47ffbccdddd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12614/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:31,601] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:31,601] [INFO] Selected 26 target genomes.
[2023-03-15 05:30:31,602] [INFO] Target genome list was writen to OceanDNA-b12614/target_genomes_gtdb.txt
[2023-03-15 05:30:31,621] [INFO] Task started: fastANI
[2023-03-15 05:30:31,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac5289a-de52-40ee-9c9c-d5e55902fbb5/OceanDNA-b12614.fa --refList OceanDNA-b12614/target_genomes_gtdb.txt --output OceanDNA-b12614/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:45,023] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:45,030] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:30:45,030] [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_905479915.1	s__GCA-002793235 sp905479915	77.0686	155	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401955.1	s__GCA-002793235 sp002401955	76.7739	156	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763135.1	s__GCA-002793235 sp016763135	76.6383	131	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002402165.1	s__GCA-002793235 sp002402165	76.5026	152	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993035.1	s__Vicingus serpentipes	76.4845	127	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359215.1	s__BRH-c54 sp002359215	76.4661	100	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	99.41	98.22	0.97	0.91	4	-
GCA_905479995.1	s__GCA-002793235 sp905479995	76.436	123	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002790175.1	s__GCA-002793235 sp002790175	76.2716	115	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	99.29	99.29	0.84	0.84	2	-
GCA_015075325.1	s__Vicingus sp015075325	76.2374	72	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	96.71	96.71	0.84	0.84	2	-
GCA_016763795.1	s__GCA-002793235 sp016763795	76.1591	122	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:45,030] [INFO] GTDB search result was written to OceanDNA-b12614/result_gtdb.tsv
[2023-03-15 05:30:45,030] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:45,031] [INFO] DFAST_QC result json was written to OceanDNA-b12614/dqc_result.json
[2023-03-15 05:30:45,031] [INFO] DFAST_QC completed!
[2023-03-15 05:30:45,031] [INFO] Total running time: 0h1m33s