[2023-03-17 09:05:02,569] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,569] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg19d678c3-047c-4840-9008-683525bb58c4/dqc_reference
[2023-03-17 09:05:03,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,729] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,729] [INFO] Running command: cat /var/lib/cwl/stg41f5219d-ff00-4f9b-828c-f93871b99199/OceanDNA-b20562.fa | prodigal -d OceanDNA-b20562/cds.fna -a OceanDNA-b20562/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:09,874] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:09,874] [INFO] Task started: HMMsearch
[2023-03-17 09:05:09,874] [INFO] Running command: hmmsearch --tblout OceanDNA-b20562/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19d678c3-047c-4840-9008-683525bb58c4/dqc_reference/reference_markers.hmm OceanDNA-b20562/protein.faa > /dev/null
[2023-03-17 09:05:10,031] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:10,032] [INFO] Found 6/6 markers.
[2023-03-17 09:05:10,043] [INFO] Query marker FASTA was written to OceanDNA-b20562/markers.fasta
[2023-03-17 09:05:10,043] [INFO] Task started: Blastn
[2023-03-17 09:05:10,043] [INFO] Running command: blastn -query OceanDNA-b20562/markers.fasta -db /var/lib/cwl/stg19d678c3-047c-4840-9008-683525bb58c4/dqc_reference/reference_markers.fasta -out OceanDNA-b20562/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:10,591] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:10,592] [INFO] Selected 19 target genomes.
[2023-03-17 09:05:10,592] [INFO] Target genome list was writen to OceanDNA-b20562/target_genomes.txt
[2023-03-17 09:05:10,671] [INFO] Task started: fastANI
[2023-03-17 09:05:10,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f5219d-ff00-4f9b-828c-f93871b99199/OceanDNA-b20562.fa --refList OceanDNA-b20562/target_genomes.txt --output OceanDNA-b20562/fastani_result.tsv --threads 1
[2023-03-17 09:05:20,200] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:20,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19d678c3-047c-4840-9008-683525bb58c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:20,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19d678c3-047c-4840-9008-683525bb58c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:20,201] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:20,201] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:05:20,201] [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 09:05:20,201] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20562/tc_result.tsv
[2023-03-17 09:05:20,201] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:20,201] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:20,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19d678c3-047c-4840-9008-683525bb58c4/dqc_reference/checkm_data
[2023-03-17 09:05:20,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:20,207] [INFO] Task started: CheckM
[2023-03-17 09:05:20,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20562/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20562/checkm_input OceanDNA-b20562/checkm_result
[2023-03-17 09:05:41,700] [INFO] Task succeeded: CheckM
[2023-03-17 09:05:41,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:05:41,702] [INFO] ===== Completeness check finished =====
[2023-03-17 09:05:41,702] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:05:41,703] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20562/markers.fasta)
[2023-03-17 09:05:41,704] [INFO] Task started: Blastn
[2023-03-17 09:05:41,704] [INFO] Running command: blastn -query OceanDNA-b20562/markers.fasta -db /var/lib/cwl/stg19d678c3-047c-4840-9008-683525bb58c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20562/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:42,613] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:42,614] [INFO] Selected 17 target genomes.
[2023-03-17 09:05:42,614] [INFO] Target genome list was writen to OceanDNA-b20562/target_genomes_gtdb.txt
[2023-03-17 09:05:42,793] [INFO] Task started: fastANI
[2023-03-17 09:05:42,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f5219d-ff00-4f9b-828c-f93871b99199/OceanDNA-b20562.fa --refList OceanDNA-b20562/target_genomes_gtdb.txt --output OceanDNA-b20562/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:05:48,234] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:48,238] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:05:48,238] [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_002707765.1	s__GCA-002718585 sp002707765	94.4908	268	413	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002718585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718585.1	s__GCA-002718585 sp002718585	93.3166	324	413	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002718585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717625.1	s__GCA-2717625 sp002717625	76.7924	114	413	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-2717625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704685.1	s__GCA-002707645 sp002704685	75.64	70	413	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:05:48,239] [INFO] GTDB search result was written to OceanDNA-b20562/result_gtdb.tsv
[2023-03-17 09:05:48,239] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:05:48,239] [INFO] DFAST_QC result json was written to OceanDNA-b20562/dqc_result.json
[2023-03-17 09:05:48,239] [INFO] DFAST_QC completed!
[2023-03-17 09:05:48,240] [INFO] Total running time: 0h0m46s