[2023-03-17 11:57:19,285] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,285] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg20758f50-b5c3-46d6-b470-c06c8af35b19/dqc_reference
[2023-03-17 11:57:20,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,891] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,891] [INFO] Running command: cat /var/lib/cwl/stg151756b5-8972-4776-90c0-94e17a3a1a82/OceanDNA-b46087.fa | prodigal -d OceanDNA-b46087/cds.fna -a OceanDNA-b46087/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:36,129] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:36,129] [INFO] Task started: HMMsearch
[2023-03-17 11:57:36,129] [INFO] Running command: hmmsearch --tblout OceanDNA-b46087/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20758f50-b5c3-46d6-b470-c06c8af35b19/dqc_reference/reference_markers.hmm OceanDNA-b46087/protein.faa > /dev/null
[2023-03-17 11:57:36,281] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:36,281] [INFO] Found 6/6 markers.
[2023-03-17 11:57:36,295] [INFO] Query marker FASTA was written to OceanDNA-b46087/markers.fasta
[2023-03-17 11:57:36,295] [INFO] Task started: Blastn
[2023-03-17 11:57:36,295] [INFO] Running command: blastn -query OceanDNA-b46087/markers.fasta -db /var/lib/cwl/stg20758f50-b5c3-46d6-b470-c06c8af35b19/dqc_reference/reference_markers.fasta -out OceanDNA-b46087/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:36,841] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:36,842] [INFO] Selected 30 target genomes.
[2023-03-17 11:57:36,842] [INFO] Target genome list was writen to OceanDNA-b46087/target_genomes.txt
[2023-03-17 11:57:36,876] [INFO] Task started: fastANI
[2023-03-17 11:57:36,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg151756b5-8972-4776-90c0-94e17a3a1a82/OceanDNA-b46087.fa --refList OceanDNA-b46087/target_genomes.txt --output OceanDNA-b46087/fastani_result.tsv --threads 1
[2023-03-17 11:57:57,021] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:57,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20758f50-b5c3-46d6-b470-c06c8af35b19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:57:57,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20758f50-b5c3-46d6-b470-c06c8af35b19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:57:57,025] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:57:57,025] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:57:57,025] [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
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.9525	102	543	95	below_threshold
Ruficoccus amylovorans	strain=JCM31066	GCA_014230085.1	1804625	1804625	type	True	76.8463	63	543	95	below_threshold
Coraliomargarita akajimensis	strain=DSM 45221	GCA_000025905.1	395922	395922	type	True	76.4884	87	543	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:57:57,026] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46087/tc_result.tsv
[2023-03-17 11:57:57,026] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:57:57,026] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:57:57,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20758f50-b5c3-46d6-b470-c06c8af35b19/dqc_reference/checkm_data
[2023-03-17 11:57:57,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:57:57,033] [INFO] Task started: CheckM
[2023-03-17 11:57:57,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46087/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46087/checkm_input OceanDNA-b46087/checkm_result
[2023-03-17 11:58:37,830] [INFO] Task succeeded: CheckM
[2023-03-17 11:58:37,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 11:58:37,832] [INFO] ===== Completeness check finished =====
[2023-03-17 11:58:37,832] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:58:37,832] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46087/markers.fasta)
[2023-03-17 11:58:37,833] [INFO] Task started: Blastn
[2023-03-17 11:58:37,833] [INFO] Running command: blastn -query OceanDNA-b46087/markers.fasta -db /var/lib/cwl/stg20758f50-b5c3-46d6-b470-c06c8af35b19/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46087/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:58:38,616] [INFO] Task succeeded: Blastn
[2023-03-17 11:58:38,617] [INFO] Selected 22 target genomes.
[2023-03-17 11:58:38,617] [INFO] Target genome list was writen to OceanDNA-b46087/target_genomes_gtdb.txt
[2023-03-17 11:58:38,773] [INFO] Task started: fastANI
[2023-03-17 11:58:38,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg151756b5-8972-4776-90c0-94e17a3a1a82/OceanDNA-b46087.fa --refList OceanDNA-b46087/target_genomes_gtdb.txt --output OceanDNA-b46087/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:58:50,951] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:50,958] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:58:50,958] [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_002469895.1	s__Coraliomargarita sp002469895	79.9852	193	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__Coraliomargarita	95.0	99.42	99.21	0.91	0.88	4	-
GCA_009908325.1	s__UBA7441 sp009908325	77.1157	79	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185655.1	s__WN38 sp003185655	76.9525	102	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879845.1	s__J108 sp014879845	76.821	53	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__J108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003566795.1	s__WN38 sp003566795	76.7488	74	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692545.1	s__UBA7441 sp007692545	76.6615	79	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402305.1	s__UBA7441 sp018402305	76.5999	64	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480015.1	s__UBA7441 sp002480015	76.5581	71	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.46	97.23	0.80	0.69	7	-
GCF_000025905.1	s__Coraliomargarita akajimensis	76.4884	87	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__Coraliomargarita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136515.1	s__CAJCBL01 sp019136515	76.3298	57	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAJCBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902728235.1	s__BACL24 sp902728235	76.0471	60	543	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.30	98.39	0.95	0.90	8	-
--------------------------------------------------------------------------------
[2023-03-17 11:58:50,958] [INFO] GTDB search result was written to OceanDNA-b46087/result_gtdb.tsv
[2023-03-17 11:58:50,958] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:58:50,960] [INFO] DFAST_QC result json was written to OceanDNA-b46087/dqc_result.json
[2023-03-17 11:58:50,960] [INFO] DFAST_QC completed!
[2023-03-17 11:58:50,960] [INFO] Total running time: 0h1m32s