[2023-03-17 23:39:58,833] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:39:58,834] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:39:58,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg692c143b-6a37-4b0b-ad76-2f0207e917fb/dqc_reference
[2023-03-17 23:39:59,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:39:59,972] [INFO] Task started: Prodigal
[2023-03-17 23:39:59,973] [INFO] Running command: cat /var/lib/cwl/stg38eb115c-8d69-4fc9-8fe2-edaf7bc665ad/OceanDNA-b46424.fa | prodigal -d OceanDNA-b46424/cds.fna -a OceanDNA-b46424/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:40:15,117] [INFO] Task succeeded: Prodigal
[2023-03-17 23:40:15,117] [INFO] Task started: HMMsearch
[2023-03-17 23:40:15,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b46424/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg692c143b-6a37-4b0b-ad76-2f0207e917fb/dqc_reference/reference_markers.hmm OceanDNA-b46424/protein.faa > /dev/null
[2023-03-17 23:40:15,282] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:40:15,283] [INFO] Found 6/6 markers.
[2023-03-17 23:40:15,300] [INFO] Query marker FASTA was written to OceanDNA-b46424/markers.fasta
[2023-03-17 23:40:15,301] [INFO] Task started: Blastn
[2023-03-17 23:40:15,301] [INFO] Running command: blastn -query OceanDNA-b46424/markers.fasta -db /var/lib/cwl/stg692c143b-6a37-4b0b-ad76-2f0207e917fb/dqc_reference/reference_markers.fasta -out OceanDNA-b46424/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:40:15,803] [INFO] Task succeeded: Blastn
[2023-03-17 23:40:15,803] [INFO] Selected 7 target genomes.
[2023-03-17 23:40:15,803] [INFO] Target genome list was writen to OceanDNA-b46424/target_genomes.txt
[2023-03-17 23:40:15,833] [INFO] Task started: fastANI
[2023-03-17 23:40:15,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg38eb115c-8d69-4fc9-8fe2-edaf7bc665ad/OceanDNA-b46424.fa --refList OceanDNA-b46424/target_genomes.txt --output OceanDNA-b46424/fastani_result.tsv --threads 1
[2023-03-17 23:40:19,436] [INFO] Task succeeded: fastANI
[2023-03-17 23:40:19,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg692c143b-6a37-4b0b-ad76-2f0207e917fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:40:19,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg692c143b-6a37-4b0b-ad76-2f0207e917fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:40:19,437] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:40:19,437] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:40:19,437] [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
--------------------------------------------------------------------------------
[2023-03-17 23:40:19,437] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46424/tc_result.tsv
[2023-03-17 23:40:19,437] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:40:19,437] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:40:19,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg692c143b-6a37-4b0b-ad76-2f0207e917fb/dqc_reference/checkm_data
[2023-03-17 23:40:19,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:40:19,444] [INFO] Task started: CheckM
[2023-03-17 23:40:19,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46424/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46424/checkm_input OceanDNA-b46424/checkm_result
[2023-03-17 23:40:58,999] [INFO] Task succeeded: CheckM
[2023-03-17 23:40:58,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.71%
Contamintation: 1.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:40:59,031] [INFO] ===== Completeness check finished =====
[2023-03-17 23:40:59,032] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:40:59,032] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46424/markers.fasta)
[2023-03-17 23:40:59,033] [INFO] Task started: Blastn
[2023-03-17 23:40:59,033] [INFO] Running command: blastn -query OceanDNA-b46424/markers.fasta -db /var/lib/cwl/stg692c143b-6a37-4b0b-ad76-2f0207e917fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46424/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:40:59,718] [INFO] Task succeeded: Blastn
[2023-03-17 23:40:59,719] [INFO] Selected 16 target genomes.
[2023-03-17 23:40:59,719] [INFO] Target genome list was writen to OceanDNA-b46424/target_genomes_gtdb.txt
[2023-03-17 23:40:59,894] [INFO] Task started: fastANI
[2023-03-17 23:40:59,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg38eb115c-8d69-4fc9-8fe2-edaf7bc665ad/OceanDNA-b46424.fa --refList OceanDNA-b46424/target_genomes_gtdb.txt --output OceanDNA-b46424/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:41:07,208] [INFO] Task succeeded: fastANI
[2023-03-17 23:41:07,211] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:41:07,211] [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	98.3573	376	608	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	97.71	97.68	0.70	0.66	3	conclusive
GCA_002684915.1	s__UBA1096 sp002684915	84.0739	461	608	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	81.8691	423	608	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.87	98.49	0.79	0.67	5	-
--------------------------------------------------------------------------------
[2023-03-17 23:41:07,212] [INFO] GTDB search result was written to OceanDNA-b46424/result_gtdb.tsv
[2023-03-17 23:41:07,212] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:41:07,212] [INFO] DFAST_QC result json was written to OceanDNA-b46424/dqc_result.json
[2023-03-17 23:41:07,212] [INFO] DFAST_QC completed!
[2023-03-17 23:41:07,212] [INFO] Total running time: 0h1m8s