[2023-03-18 21:43:12,588] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:43:12,589] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:43:12,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg95d8ab41-14f5-43ad-9e7b-58579f23c515/dqc_reference
[2023-03-18 21:43:13,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:43:13,746] [INFO] Task started: Prodigal
[2023-03-18 21:43:13,746] [INFO] Running command: cat /var/lib/cwl/stge5d07244-1096-4516-a328-d37c8af4f87d/OceanDNA-b12632.fa | prodigal -d OceanDNA-b12632/cds.fna -a OceanDNA-b12632/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:43:31,575] [INFO] Task succeeded: Prodigal
[2023-03-18 21:43:31,576] [INFO] Task started: HMMsearch
[2023-03-18 21:43:31,576] [INFO] Running command: hmmsearch --tblout OceanDNA-b12632/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95d8ab41-14f5-43ad-9e7b-58579f23c515/dqc_reference/reference_markers.hmm OceanDNA-b12632/protein.faa > /dev/null
[2023-03-18 21:43:31,768] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:43:31,768] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge5d07244-1096-4516-a328-d37c8af4f87d/OceanDNA-b12632.fa]
[2023-03-18 21:43:31,788] [INFO] Query marker FASTA was written to OceanDNA-b12632/markers.fasta
[2023-03-18 21:43:31,789] [INFO] Task started: Blastn
[2023-03-18 21:43:31,789] [INFO] Running command: blastn -query OceanDNA-b12632/markers.fasta -db /var/lib/cwl/stg95d8ab41-14f5-43ad-9e7b-58579f23c515/dqc_reference/reference_markers.fasta -out OceanDNA-b12632/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:43:32,312] [INFO] Task succeeded: Blastn
[2023-03-18 21:43:32,313] [INFO] Selected 28 target genomes.
[2023-03-18 21:43:32,313] [INFO] Target genome list was writen to OceanDNA-b12632/target_genomes.txt
[2023-03-18 21:43:32,326] [INFO] Task started: fastANI
[2023-03-18 21:43:32,326] [INFO] Running command: fastANI --query /var/lib/cwl/stge5d07244-1096-4516-a328-d37c8af4f87d/OceanDNA-b12632.fa --refList OceanDNA-b12632/target_genomes.txt --output OceanDNA-b12632/fastani_result.tsv --threads 1
[2023-03-18 21:43:47,021] [INFO] Task succeeded: fastANI
[2023-03-18 21:43:47,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95d8ab41-14f5-43ad-9e7b-58579f23c515/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:43:47,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95d8ab41-14f5-43ad-9e7b-58579f23c515/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:43:47,025] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:43:47,025] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:43:47,025] [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
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.182	61	948	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:43:47,025] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12632/tc_result.tsv
[2023-03-18 21:43:47,026] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:43:47,026] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:43:47,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95d8ab41-14f5-43ad-9e7b-58579f23c515/dqc_reference/checkm_data
[2023-03-18 21:43:47,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:43:47,031] [INFO] Task started: CheckM
[2023-03-18 21:43:47,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12632/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12632/checkm_input OceanDNA-b12632/checkm_result
[2023-03-18 21:44:32,824] [INFO] Task succeeded: CheckM
[2023-03-18 21:44:32,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:44:32,827] [INFO] ===== Completeness check finished =====
[2023-03-18 21:44:32,827] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:44:32,827] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12632/markers.fasta)
[2023-03-18 21:44:32,828] [INFO] Task started: Blastn
[2023-03-18 21:44:32,828] [INFO] Running command: blastn -query OceanDNA-b12632/markers.fasta -db /var/lib/cwl/stg95d8ab41-14f5-43ad-9e7b-58579f23c515/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12632/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:44:33,566] [INFO] Task succeeded: Blastn
[2023-03-18 21:44:33,567] [INFO] Selected 19 target genomes.
[2023-03-18 21:44:33,567] [INFO] Target genome list was writen to OceanDNA-b12632/target_genomes_gtdb.txt
[2023-03-18 21:44:33,580] [INFO] Task started: fastANI
[2023-03-18 21:44:33,580] [INFO] Running command: fastANI --query /var/lib/cwl/stge5d07244-1096-4516-a328-d37c8af4f87d/OceanDNA-b12632.fa --refList OceanDNA-b12632/target_genomes_gtdb.txt --output OceanDNA-b12632/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:44:42,946] [INFO] Task succeeded: fastANI
[2023-03-18 21:44:42,953] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:44:42,953] [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_016763795.1	s__GCA-002793235 sp016763795	78.9284	366	948	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	78.7451	345	948	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_905479915.1	s__GCA-002793235 sp905479915	78.5227	342	948	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	77.2882	250	948	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	77.2417	256	948	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_905479995.1	s__GCA-002793235 sp905479995	76.9938	192	948	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	76.9228	163	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002790175.1	s__GCA-002793235 sp002790175	76.2463	124	948	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_000961845.1	s__BRH-c54 sp000961845	76.1093	95	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841035.1	s__BRH-c54 sp002841035	75.5425	68	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:44:42,954] [INFO] GTDB search result was written to OceanDNA-b12632/result_gtdb.tsv
[2023-03-18 21:44:42,954] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:44:42,955] [INFO] DFAST_QC result json was written to OceanDNA-b12632/dqc_result.json
[2023-03-18 21:44:42,955] [INFO] DFAST_QC completed!
[2023-03-18 21:44:42,955] [INFO] Total running time: 0h1m30s