[2023-03-15 13:52:04,713] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:52:04,713] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:52:04,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg696a1a99-fcdd-4a91-b925-21acf8ca9a64/dqc_reference
[2023-03-15 13:52:05,800] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:52:05,806] [INFO] Task started: Prodigal
[2023-03-15 13:52:05,806] [INFO] Running command: cat /var/lib/cwl/stged196ecb-9132-4d29-8b05-7b1a41f6fc9e/OceanDNA-b46427.fa | prodigal -d OceanDNA-b46427/cds.fna -a OceanDNA-b46427/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:52:26,187] [INFO] Task succeeded: Prodigal
[2023-03-15 13:52:26,187] [INFO] Task started: HMMsearch
[2023-03-15 13:52:26,187] [INFO] Running command: hmmsearch --tblout OceanDNA-b46427/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg696a1a99-fcdd-4a91-b925-21acf8ca9a64/dqc_reference/reference_markers.hmm OceanDNA-b46427/protein.faa > /dev/null
[2023-03-15 13:52:26,383] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:52:26,384] [INFO] Found 6/6 markers.
[2023-03-15 13:52:26,403] [INFO] Query marker FASTA was written to OceanDNA-b46427/markers.fasta
[2023-03-15 13:52:26,404] [INFO] Task started: Blastn
[2023-03-15 13:52:26,404] [INFO] Running command: blastn -query OceanDNA-b46427/markers.fasta -db /var/lib/cwl/stg696a1a99-fcdd-4a91-b925-21acf8ca9a64/dqc_reference/reference_markers.fasta -out OceanDNA-b46427/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:52:26,923] [INFO] Task succeeded: Blastn
[2023-03-15 13:52:26,923] [INFO] Selected 10 target genomes.
[2023-03-15 13:52:26,924] [INFO] Target genome list was writen to OceanDNA-b46427/target_genomes.txt
[2023-03-15 13:52:26,930] [INFO] Task started: fastANI
[2023-03-15 13:52:26,930] [INFO] Running command: fastANI --query /var/lib/cwl/stged196ecb-9132-4d29-8b05-7b1a41f6fc9e/OceanDNA-b46427.fa --refList OceanDNA-b46427/target_genomes.txt --output OceanDNA-b46427/fastani_result.tsv --threads 1
[2023-03-15 13:52:31,515] [INFO] Task succeeded: fastANI
[2023-03-15 13:52:31,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg696a1a99-fcdd-4a91-b925-21acf8ca9a64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:52:31,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg696a1a99-fcdd-4a91-b925-21acf8ca9a64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:52:31,516] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:52:31,516] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:52:31,516] [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
--------------------------------------------------------------------------------
[2023-03-15 13:52:31,517] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46427/tc_result.tsv
[2023-03-15 13:52:31,517] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:52:31,517] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:52:31,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg696a1a99-fcdd-4a91-b925-21acf8ca9a64/dqc_reference/checkm_data
[2023-03-15 13:52:31,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:52:31,525] [INFO] Task started: CheckM
[2023-03-15 13:52:31,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46427/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46427/checkm_input OceanDNA-b46427/checkm_result
[2023-03-15 13:53:25,717] [INFO] Task succeeded: CheckM
[2023-03-15 13:53:25,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:53:25,738] [INFO] ===== Completeness check finished =====
[2023-03-15 13:53:25,739] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:53:25,739] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46427/markers.fasta)
[2023-03-15 13:53:25,740] [INFO] Task started: Blastn
[2023-03-15 13:53:25,740] [INFO] Running command: blastn -query OceanDNA-b46427/markers.fasta -db /var/lib/cwl/stg696a1a99-fcdd-4a91-b925-21acf8ca9a64/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46427/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:53:26,670] [INFO] Task succeeded: Blastn
[2023-03-15 13:53:26,672] [INFO] Selected 20 target genomes.
[2023-03-15 13:53:26,672] [INFO] Target genome list was writen to OceanDNA-b46427/target_genomes_gtdb.txt
[2023-03-15 13:53:26,687] [INFO] Task started: fastANI
[2023-03-15 13:53:26,687] [INFO] Running command: fastANI --query /var/lib/cwl/stged196ecb-9132-4d29-8b05-7b1a41f6fc9e/OceanDNA-b46427.fa --refList OceanDNA-b46427/target_genomes_gtdb.txt --output OceanDNA-b46427/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:53:37,167] [INFO] Task succeeded: fastANI
[2023-03-15 13:53:37,171] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:53:37,171] [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_002708005.1	s__UBA1096 sp002708005	79.0662	320	930	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	97.71	97.68	0.70	0.66	3	-
GCA_002684915.1	s__UBA1096 sp002684915	78.8744	444	930	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.82	98.82	0.77	0.77	2	-
GCA_004213515.1	s__UBA1096 sp002170545	78.5054	373	930	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.87	98.49	0.79	0.67	5	-
GCA_002453165.1	s__UBA1096 sp002453165	76.6125	73	930	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	96.70	95.18	0.81	0.76	7	-
--------------------------------------------------------------------------------
[2023-03-15 13:53:37,171] [INFO] GTDB search result was written to OceanDNA-b46427/result_gtdb.tsv
[2023-03-15 13:53:37,171] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:53:37,172] [INFO] DFAST_QC result json was written to OceanDNA-b46427/dqc_result.json
[2023-03-15 13:53:37,172] [INFO] DFAST_QC completed!
[2023-03-15 13:53:37,172] [INFO] Total running time: 0h1m32s