[2023-03-16 05:07:01,487] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:07:01,487] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:07:01,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a493af4-6627-486f-bd18-cc3416a2254e/dqc_reference
[2023-03-16 05:07:04,494] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:07:04,496] [INFO] Task started: Prodigal
[2023-03-16 05:07:04,496] [INFO] Running command: cat /var/lib/cwl/stg2bb716fd-fcfd-4711-bb80-7dcbd6e12640/OceanDNA-b4028.fa | prodigal -d OceanDNA-b4028/cds.fna -a OceanDNA-b4028/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:07:31,569] [INFO] Task succeeded: Prodigal
[2023-03-16 05:07:31,569] [INFO] Task started: HMMsearch
[2023-03-16 05:07:31,569] [INFO] Running command: hmmsearch --tblout OceanDNA-b4028/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a493af4-6627-486f-bd18-cc3416a2254e/dqc_reference/reference_markers.hmm OceanDNA-b4028/protein.faa > /dev/null
[2023-03-16 05:07:31,774] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:07:31,774] [INFO] Found 6/6 markers.
[2023-03-16 05:07:31,801] [INFO] Query marker FASTA was written to OceanDNA-b4028/markers.fasta
[2023-03-16 05:07:31,802] [INFO] Task started: Blastn
[2023-03-16 05:07:31,802] [INFO] Running command: blastn -query OceanDNA-b4028/markers.fasta -db /var/lib/cwl/stg8a493af4-6627-486f-bd18-cc3416a2254e/dqc_reference/reference_markers.fasta -out OceanDNA-b4028/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:07:32,317] [INFO] Task succeeded: Blastn
[2023-03-16 05:07:32,318] [INFO] Selected 25 target genomes.
[2023-03-16 05:07:32,319] [INFO] Target genome list was writen to OceanDNA-b4028/target_genomes.txt
[2023-03-16 05:07:32,334] [INFO] Task started: fastANI
[2023-03-16 05:07:32,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bb716fd-fcfd-4711-bb80-7dcbd6e12640/OceanDNA-b4028.fa --refList OceanDNA-b4028/target_genomes.txt --output OceanDNA-b4028/fastani_result.tsv --threads 1
[2023-03-16 05:07:53,332] [INFO] Task succeeded: fastANI
[2023-03-16 05:07:53,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a493af4-6627-486f-bd18-cc3416a2254e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:07:53,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a493af4-6627-486f-bd18-cc3416a2254e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:07:53,337] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:07:53,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:07:53,338] [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
Chryseotalea sanaruensis	strain=Ys	GCA_003990915.1	2482724	2482724	type	True	75.5993	55	1193	95	below_threshold
Ohtaekwangia koreensis	strain=DSM 25262	GCA_900167975.1	688867	688867	type	True	75.5184	52	1193	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:07:53,338] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4028/tc_result.tsv
[2023-03-16 05:07:53,338] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:07:53,338] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:07:53,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a493af4-6627-486f-bd18-cc3416a2254e/dqc_reference/checkm_data
[2023-03-16 05:07:53,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:07:53,344] [INFO] Task started: CheckM
[2023-03-16 05:07:53,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4028/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4028/checkm_input OceanDNA-b4028/checkm_result
[2023-03-16 05:09:00,611] [INFO] Task succeeded: CheckM
[2023-03-16 05:09:00,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:09:00,614] [INFO] ===== Completeness check finished =====
[2023-03-16 05:09:00,615] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:09:00,615] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4028/markers.fasta)
[2023-03-16 05:09:00,616] [INFO] Task started: Blastn
[2023-03-16 05:09:00,616] [INFO] Running command: blastn -query OceanDNA-b4028/markers.fasta -db /var/lib/cwl/stg8a493af4-6627-486f-bd18-cc3416a2254e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4028/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:09:01,300] [INFO] Task succeeded: Blastn
[2023-03-16 05:09:01,301] [INFO] Selected 19 target genomes.
[2023-03-16 05:09:01,301] [INFO] Target genome list was writen to OceanDNA-b4028/target_genomes_gtdb.txt
[2023-03-16 05:09:01,324] [INFO] Task started: fastANI
[2023-03-16 05:09:01,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bb716fd-fcfd-4711-bb80-7dcbd6e12640/OceanDNA-b4028.fa --refList OceanDNA-b4028/target_genomes_gtdb.txt --output OceanDNA-b4028/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:09:14,815] [INFO] Task succeeded: fastANI
[2023-03-16 05:09:14,826] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:09:14,826] [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_016787755.1	s__ELB16-189 sp016787755	81.9116	779	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787745.1	s__ELB16-189 sp016787745	77.3918	180	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712035.1	s__ELB16-189 sp016712035	77.1019	252	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709845.1	s__ELB16-189 sp016709845	77.069	238	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018063305.1	s__ELB16-189 sp018063305	76.9144	186	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303795.1	s__ELB16-189 sp017303795	76.825	207	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650355.1	s__ELB16-189 sp016650355	76.7404	64	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303805.1	s__ELB16-189 sp017303805	76.4394	125	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298505.1	s__ELB16-189 sp013298505	76.2885	94	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013414665.1	s__ELB16-189 sp013414665	76.1206	148	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003537495.1	s__ELB16-189 sp003537495	76.1153	129	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787725.1	s__ELB16-189 sp016787725	75.9304	133	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140395.1	s__ELB16-189 sp013140395	75.7106	51	1193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:09:14,827] [INFO] GTDB search result was written to OceanDNA-b4028/result_gtdb.tsv
[2023-03-16 05:09:14,827] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:09:14,829] [INFO] DFAST_QC result json was written to OceanDNA-b4028/dqc_result.json
[2023-03-16 05:09:14,829] [INFO] DFAST_QC completed!
[2023-03-16 05:09:14,829] [INFO] Total running time: 0h2m13s