[2023-03-19 02:49:38,482] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:49:38,482] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:49:38,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg04ad5f73-7023-443d-8b70-6a13c2478d1f/dqc_reference
[2023-03-19 02:49:39,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:49:39,607] [INFO] Task started: Prodigal
[2023-03-19 02:49:39,607] [INFO] Running command: cat /var/lib/cwl/stgeb117578-d7e5-478d-b382-9c0a4bd86825/OceanDNA-b46391.fa | prodigal -d OceanDNA-b46391/cds.fna -a OceanDNA-b46391/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:50:09,892] [INFO] Task succeeded: Prodigal
[2023-03-19 02:50:09,892] [INFO] Task started: HMMsearch
[2023-03-19 02:50:09,892] [INFO] Running command: hmmsearch --tblout OceanDNA-b46391/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04ad5f73-7023-443d-8b70-6a13c2478d1f/dqc_reference/reference_markers.hmm OceanDNA-b46391/protein.faa > /dev/null
[2023-03-19 02:50:10,077] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:50:10,077] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeb117578-d7e5-478d-b382-9c0a4bd86825/OceanDNA-b46391.fa]
[2023-03-19 02:50:10,104] [INFO] Query marker FASTA was written to OceanDNA-b46391/markers.fasta
[2023-03-19 02:50:10,106] [INFO] Task started: Blastn
[2023-03-19 02:50:10,106] [INFO] Running command: blastn -query OceanDNA-b46391/markers.fasta -db /var/lib/cwl/stg04ad5f73-7023-443d-8b70-6a13c2478d1f/dqc_reference/reference_markers.fasta -out OceanDNA-b46391/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:50:10,672] [INFO] Task succeeded: Blastn
[2023-03-19 02:50:10,673] [INFO] Selected 17 target genomes.
[2023-03-19 02:50:10,673] [INFO] Target genome list was writen to OceanDNA-b46391/target_genomes.txt
[2023-03-19 02:50:10,680] [INFO] Task started: fastANI
[2023-03-19 02:50:10,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb117578-d7e5-478d-b382-9c0a4bd86825/OceanDNA-b46391.fa --refList OceanDNA-b46391/target_genomes.txt --output OceanDNA-b46391/fastani_result.tsv --threads 1
[2023-03-19 02:50:22,338] [INFO] Task succeeded: fastANI
[2023-03-19 02:50:22,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04ad5f73-7023-443d-8b70-6a13c2478d1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:50:22,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04ad5f73-7023-443d-8b70-6a13c2478d1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:50:22,339] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:50:22,339] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:50:22,339] [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
--------------------------------------------------------------------------------
[2023-03-19 02:50:22,339] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46391/tc_result.tsv
[2023-03-19 02:50:22,340] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:50:22,340] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:50:22,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04ad5f73-7023-443d-8b70-6a13c2478d1f/dqc_reference/checkm_data
[2023-03-19 02:50:22,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:50:22,357] [INFO] Task started: CheckM
[2023-03-19 02:50:22,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46391/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46391/checkm_input OceanDNA-b46391/checkm_result
[2023-03-19 02:51:38,821] [INFO] Task succeeded: CheckM
[2023-03-19 02:51:38,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:51:38,828] [INFO] ===== Completeness check finished =====
[2023-03-19 02:51:38,828] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:51:38,828] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46391/markers.fasta)
[2023-03-19 02:51:38,829] [INFO] Task started: Blastn
[2023-03-19 02:51:38,829] [INFO] Running command: blastn -query OceanDNA-b46391/markers.fasta -db /var/lib/cwl/stg04ad5f73-7023-443d-8b70-6a13c2478d1f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46391/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:51:39,705] [INFO] Task succeeded: Blastn
[2023-03-19 02:51:39,706] [INFO] Selected 6 target genomes.
[2023-03-19 02:51:39,706] [INFO] Target genome list was writen to OceanDNA-b46391/target_genomes_gtdb.txt
[2023-03-19 02:51:39,711] [INFO] Task started: fastANI
[2023-03-19 02:51:39,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb117578-d7e5-478d-b382-9c0a4bd86825/OceanDNA-b46391.fa --refList OceanDNA-b46391/target_genomes_gtdb.txt --output OceanDNA-b46391/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:51:43,756] [INFO] Task succeeded: fastANI
[2023-03-19 02:51:43,761] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:51:43,761] [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_018674955.1	s__UBA1096 sp018674955	98.8404	792	977	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.88	98.74	0.86	0.81	14	conclusive
GCA_015658765.1	s__UBA1096 sp015658765	90.4963	402	977	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299785.1	s__UBA1096 sp002299785	88.6174	436	977	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972865.1	s__UBA1096 sp003972865	86.0264	496	977	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382705.1	s__UBA1096 sp014382705	84.1792	648	977	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686755.1	s__UBA1096 sp002686755	82.4956	538	977	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:51:43,763] [INFO] GTDB search result was written to OceanDNA-b46391/result_gtdb.tsv
[2023-03-19 02:51:43,765] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:51:43,768] [INFO] DFAST_QC result json was written to OceanDNA-b46391/dqc_result.json
[2023-03-19 02:51:43,768] [INFO] DFAST_QC completed!
[2023-03-19 02:51:43,768] [INFO] Total running time: 0h2m5s