[2023-03-15 22:44:22,101] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,103] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg19dbc6dc-ea53-4ca9-9beb-cb70f0dcf905/dqc_reference
[2023-03-15 22:44:23,186] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,187] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,187] [INFO] Running command: cat /var/lib/cwl/stg7ad3bb60-9744-44ec-b072-864eae74b600/OceanDNA-b111.fa | prodigal -d OceanDNA-b111/cds.fna -a OceanDNA-b111/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:35,984] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:35,985] [INFO] Task started: HMMsearch
[2023-03-15 22:44:35,985] [INFO] Running command: hmmsearch --tblout OceanDNA-b111/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19dbc6dc-ea53-4ca9-9beb-cb70f0dcf905/dqc_reference/reference_markers.hmm OceanDNA-b111/protein.faa > /dev/null
[2023-03-15 22:44:36,195] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:36,195] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7ad3bb60-9744-44ec-b072-864eae74b600/OceanDNA-b111.fa]
[2023-03-15 22:44:36,231] [INFO] Query marker FASTA was written to OceanDNA-b111/markers.fasta
[2023-03-15 22:44:36,232] [INFO] Task started: Blastn
[2023-03-15 22:44:36,232] [INFO] Running command: blastn -query OceanDNA-b111/markers.fasta -db /var/lib/cwl/stg19dbc6dc-ea53-4ca9-9beb-cb70f0dcf905/dqc_reference/reference_markers.fasta -out OceanDNA-b111/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:36,850] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:36,860] [INFO] Selected 29 target genomes.
[2023-03-15 22:44:36,860] [INFO] Target genome list was writen to OceanDNA-b111/target_genomes.txt
[2023-03-15 22:44:36,874] [INFO] Task started: fastANI
[2023-03-15 22:44:36,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad3bb60-9744-44ec-b072-864eae74b600/OceanDNA-b111.fa --refList OceanDNA-b111/target_genomes.txt --output OceanDNA-b111/fastani_result.tsv --threads 1
[2023-03-15 22:44:56,062] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:56,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19dbc6dc-ea53-4ca9-9beb-cb70f0dcf905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:44:56,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19dbc6dc-ea53-4ca9-9beb-cb70f0dcf905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:44:56,066] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:44:56,066] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:44:56,066] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	76.1981	82	598	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.9323	53	598	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:44:56,073] [INFO] DFAST Taxonomy check result was written to OceanDNA-b111/tc_result.tsv
[2023-03-15 22:44:56,093] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:44:56,094] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:44:56,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19dbc6dc-ea53-4ca9-9beb-cb70f0dcf905/dqc_reference/checkm_data
[2023-03-15 22:44:56,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:44:56,120] [INFO] Task started: CheckM
[2023-03-15 22:44:56,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b111/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b111/checkm_input OceanDNA-b111/checkm_result
[2023-03-15 22:45:31,582] [INFO] Task succeeded: CheckM
[2023-03-15 22:45:31,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.77%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:45:31,783] [INFO] ===== Completeness check finished =====
[2023-03-15 22:45:31,784] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:45:31,784] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b111/markers.fasta)
[2023-03-15 22:45:31,785] [INFO] Task started: Blastn
[2023-03-15 22:45:31,785] [INFO] Running command: blastn -query OceanDNA-b111/markers.fasta -db /var/lib/cwl/stg19dbc6dc-ea53-4ca9-9beb-cb70f0dcf905/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b111/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:45:32,826] [INFO] Task succeeded: Blastn
[2023-03-15 22:45:32,833] [INFO] Selected 17 target genomes.
[2023-03-15 22:45:32,833] [INFO] Target genome list was writen to OceanDNA-b111/target_genomes_gtdb.txt
[2023-03-15 22:45:33,014] [INFO] Task started: fastANI
[2023-03-15 22:45:33,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad3bb60-9744-44ec-b072-864eae74b600/OceanDNA-b111.fa --refList OceanDNA-b111/target_genomes_gtdb.txt --output OceanDNA-b111/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:45:46,374] [INFO] Task succeeded: fastANI
[2023-03-15 22:45:46,383] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:45:46,383] [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_001768615.1	s__12-FULL-67-14b sp001768615	79.9144	322	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737365.1	s__12-FULL-67-14b sp002737365	79.0117	224	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	97.27	96.58	0.83	0.80	6	-
GCA_009694735.1	s__12-FULL-67-14b sp009694735	78.6879	225	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871275.1	s__12-FULL-67-14b sp016871275	78.2695	219	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018000455.1	s__CADEFD01 sp018000455	77.1948	179	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789705.1	s__CADEFD01 sp016789705	77.1818	158	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871375.1	s__Gp6-AA40 sp016871375	76.9229	97	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826515.1	s__CADEFD01 sp902826515	76.8134	180	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650245.1	s__JAENWD01 sp016650245	76.8022	71	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JAENWD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871195.1	s__VFZN01 sp016871195	76.5175	91	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767525.1	s__Gp6-AA40 sp001767525	76.303	86	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.96	99.96	0.95	0.95	2	-
GCA_001724025.1	s__SCN-69-37 sp001724025	76.1105	65	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SCN-69-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789685.1	s__JAEUQQ01 sp016789685	76.0397	89	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__JAFNAJ01;g__JAEUQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825985.1	s__WHSN01 sp902825985	75.9756	88	598	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:45:46,392] [INFO] GTDB search result was written to OceanDNA-b111/result_gtdb.tsv
[2023-03-15 22:45:46,403] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:45:46,414] [INFO] DFAST_QC result json was written to OceanDNA-b111/dqc_result.json
[2023-03-15 22:45:46,414] [INFO] DFAST_QC completed!
[2023-03-15 22:45:46,414] [INFO] Total running time: 0h1m24s