[2023-03-18 23:40:00,434] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:40:00,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:40:00,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5c617d2-377f-40ab-a722-700b254bf4b7/dqc_reference
[2023-03-18 23:40:01,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:40:01,548] [INFO] Task started: Prodigal
[2023-03-18 23:40:01,548] [INFO] Running command: cat /var/lib/cwl/stgf37a0277-336c-4c09-a0f3-4206301912eb/OceanDNA-b5391.fa | prodigal -d OceanDNA-b5391/cds.fna -a OceanDNA-b5391/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:40:17,430] [INFO] Task succeeded: Prodigal
[2023-03-18 23:40:17,431] [INFO] Task started: HMMsearch
[2023-03-18 23:40:17,431] [INFO] Running command: hmmsearch --tblout OceanDNA-b5391/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5c617d2-377f-40ab-a722-700b254bf4b7/dqc_reference/reference_markers.hmm OceanDNA-b5391/protein.faa > /dev/null
[2023-03-18 23:40:17,633] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:40:17,634] [INFO] Found 6/6 markers.
[2023-03-18 23:40:17,650] [INFO] Query marker FASTA was written to OceanDNA-b5391/markers.fasta
[2023-03-18 23:40:17,650] [INFO] Task started: Blastn
[2023-03-18 23:40:17,650] [INFO] Running command: blastn -query OceanDNA-b5391/markers.fasta -db /var/lib/cwl/stgc5c617d2-377f-40ab-a722-700b254bf4b7/dqc_reference/reference_markers.fasta -out OceanDNA-b5391/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:18,187] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:18,188] [INFO] Selected 23 target genomes.
[2023-03-18 23:40:18,189] [INFO] Target genome list was writen to OceanDNA-b5391/target_genomes.txt
[2023-03-18 23:40:18,201] [INFO] Task started: fastANI
[2023-03-18 23:40:18,201] [INFO] Running command: fastANI --query /var/lib/cwl/stgf37a0277-336c-4c09-a0f3-4206301912eb/OceanDNA-b5391.fa --refList OceanDNA-b5391/target_genomes.txt --output OceanDNA-b5391/fastani_result.tsv --threads 1
[2023-03-18 23:40:31,925] [INFO] Task succeeded: fastANI
[2023-03-18 23:40:31,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5c617d2-377f-40ab-a722-700b254bf4b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:40:31,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5c617d2-377f-40ab-a722-700b254bf4b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:40:31,929] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:40:31,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:40:31,929] [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
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	76.0005	51	786	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:40:31,929] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5391/tc_result.tsv
[2023-03-18 23:40:31,929] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:40:31,929] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:40:31,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5c617d2-377f-40ab-a722-700b254bf4b7/dqc_reference/checkm_data
[2023-03-18 23:40:31,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:40:31,935] [INFO] Task started: CheckM
[2023-03-18 23:40:31,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5391/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5391/checkm_input OceanDNA-b5391/checkm_result
[2023-03-18 23:41:15,538] [INFO] Task succeeded: CheckM
[2023-03-18 23:41:15,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:41:15,541] [INFO] ===== Completeness check finished =====
[2023-03-18 23:41:15,541] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:41:15,542] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5391/markers.fasta)
[2023-03-18 23:41:15,543] [INFO] Task started: Blastn
[2023-03-18 23:41:15,543] [INFO] Running command: blastn -query OceanDNA-b5391/markers.fasta -db /var/lib/cwl/stgc5c617d2-377f-40ab-a722-700b254bf4b7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5391/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:41:16,572] [INFO] Task succeeded: Blastn
[2023-03-18 23:41:16,573] [INFO] Selected 21 target genomes.
[2023-03-18 23:41:16,573] [INFO] Target genome list was writen to OceanDNA-b5391/target_genomes_gtdb.txt
[2023-03-18 23:41:16,585] [INFO] Task started: fastANI
[2023-03-18 23:41:16,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgf37a0277-336c-4c09-a0f3-4206301912eb/OceanDNA-b5391.fa --refList OceanDNA-b5391/target_genomes_gtdb.txt --output OceanDNA-b5391/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:41:26,881] [INFO] Task succeeded: fastANI
[2023-03-18 23:41:26,888] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:41:26,888] [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_905480355.1	s__UBA4466 sp002389415	99.4855	641	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.55	99.55	0.81	0.81	2	conclusive
GCA_905480145.1	s__UBA4466 sp905480145	78.0749	183	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002734065.2	s__UBA4466 sp002734065	77.4382	165	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471375.1	s__UBA4466 sp002471375	77.2557	63	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402525.1	s__UBA4466 sp018402525	77.1505	64	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182335.1	s__UBA4466 sp905182335	77.0373	96	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.88	99.88	0.98	0.98	2	-
GCA_013215515.1	s__UBA4466 sp013215515	76.6159	71	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478665.1	s__UBA4466 sp905478665	76.5893	77	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709305.1	s__UBA4466 sp002709305	76.4936	63	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427735.1	s__UBA4466 sp002427735	76.0625	61	786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:41:26,888] [INFO] GTDB search result was written to OceanDNA-b5391/result_gtdb.tsv
[2023-03-18 23:41:26,888] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:41:26,890] [INFO] DFAST_QC result json was written to OceanDNA-b5391/dqc_result.json
[2023-03-18 23:41:26,890] [INFO] DFAST_QC completed!
[2023-03-18 23:41:26,890] [INFO] Total running time: 0h1m26s