[2023-03-15 14:47:21,402] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:47:21,407] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:47:21,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c27c3f0-5f18-4a45-9786-47355822689b/dqc_reference
[2023-03-15 14:47:22,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:47:22,557] [INFO] Task started: Prodigal
[2023-03-15 14:47:22,558] [INFO] Running command: cat /var/lib/cwl/stg87172f16-a0ee-4f68-a034-db27aace8900/OceanDNA-b45667.fa | prodigal -d OceanDNA-b45667/cds.fna -a OceanDNA-b45667/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:47:36,519] [INFO] Task succeeded: Prodigal
[2023-03-15 14:47:36,519] [INFO] Task started: HMMsearch
[2023-03-15 14:47:36,519] [INFO] Running command: hmmsearch --tblout OceanDNA-b45667/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c27c3f0-5f18-4a45-9786-47355822689b/dqc_reference/reference_markers.hmm OceanDNA-b45667/protein.faa > /dev/null
[2023-03-15 14:47:36,683] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:47:36,684] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg87172f16-a0ee-4f68-a034-db27aace8900/OceanDNA-b45667.fa]
[2023-03-15 14:47:36,731] [INFO] Query marker FASTA was written to OceanDNA-b45667/markers.fasta
[2023-03-15 14:47:36,732] [INFO] Task started: Blastn
[2023-03-15 14:47:36,733] [INFO] Running command: blastn -query OceanDNA-b45667/markers.fasta -db /var/lib/cwl/stg1c27c3f0-5f18-4a45-9786-47355822689b/dqc_reference/reference_markers.fasta -out OceanDNA-b45667/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:47:37,221] [INFO] Task succeeded: Blastn
[2023-03-15 14:47:37,235] [INFO] Selected 5 target genomes.
[2023-03-15 14:47:37,235] [INFO] Target genome list was writen to OceanDNA-b45667/target_genomes.txt
[2023-03-15 14:47:37,240] [INFO] Task started: fastANI
[2023-03-15 14:47:37,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg87172f16-a0ee-4f68-a034-db27aace8900/OceanDNA-b45667.fa --refList OceanDNA-b45667/target_genomes.txt --output OceanDNA-b45667/fastani_result.tsv --threads 1
[2023-03-15 14:47:39,206] [INFO] Task succeeded: fastANI
[2023-03-15 14:47:39,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c27c3f0-5f18-4a45-9786-47355822689b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:47:39,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c27c3f0-5f18-4a45-9786-47355822689b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:47:39,206] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:47:39,206] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:47:39,206] [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 14:47:39,211] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45667/tc_result.tsv
[2023-03-15 14:47:39,219] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:47:39,219] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:47:39,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c27c3f0-5f18-4a45-9786-47355822689b/dqc_reference/checkm_data
[2023-03-15 14:47:39,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:47:39,284] [INFO] Task started: CheckM
[2023-03-15 14:47:39,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45667/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45667/checkm_input OceanDNA-b45667/checkm_result
[2023-03-15 14:48:18,049] [INFO] Task succeeded: CheckM
[2023-03-15 14:48:18,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:48:18,071] [INFO] ===== Completeness check finished =====
[2023-03-15 14:48:18,071] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:48:18,072] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45667/markers.fasta)
[2023-03-15 14:48:18,074] [INFO] Task started: Blastn
[2023-03-15 14:48:18,074] [INFO] Running command: blastn -query OceanDNA-b45667/markers.fasta -db /var/lib/cwl/stg1c27c3f0-5f18-4a45-9786-47355822689b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45667/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:48:18,711] [INFO] Task succeeded: Blastn
[2023-03-15 14:48:18,718] [INFO] Selected 12 target genomes.
[2023-03-15 14:48:18,718] [INFO] Target genome list was writen to OceanDNA-b45667/target_genomes_gtdb.txt
[2023-03-15 14:48:18,777] [INFO] Task started: fastANI
[2023-03-15 14:48:18,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg87172f16-a0ee-4f68-a034-db27aace8900/OceanDNA-b45667.fa --refList OceanDNA-b45667/target_genomes_gtdb.txt --output OceanDNA-b45667/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:48:23,510] [INFO] Task succeeded: fastANI
[2023-03-15 14:48:23,515] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:48:23,515] [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_002168015.1	s__MB11C04 sp002168015	79.3797	180	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478775.1	s__MB11C04 sp002477515	78.6728	51	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.93	98.38	0.86	0.80	5	-
GCA_002167265.1	s__MB11C04 sp002167265	77.345	77	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689665.1	s__MB11C04 sp002689665	77.3064	86	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675995.1	s__MB11C04 sp018675995	77.0572	56	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694035.1	s__MB11C04 sp002694035	76.3	50	634	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:48:23,518] [INFO] GTDB search result was written to OceanDNA-b45667/result_gtdb.tsv
[2023-03-15 14:48:23,523] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:48:23,528] [INFO] DFAST_QC result json was written to OceanDNA-b45667/dqc_result.json
[2023-03-15 14:48:23,528] [INFO] DFAST_QC completed!
[2023-03-15 14:48:23,528] [INFO] Total running time: 0h1m2s