[2023-03-15 08:59:49,031] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:49,031] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:49,031] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a973595-cd24-43ca-8620-90883a3a121c/dqc_reference
[2023-03-15 08:59:50,118] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:50,118] [INFO] Task started: Prodigal
[2023-03-15 08:59:50,118] [INFO] Running command: cat /var/lib/cwl/stg9f84621c-0b5f-4c7b-97b4-e5e6f8e4280d/OceanDNA-b19450.fa | prodigal -d OceanDNA-b19450/cds.fna -a OceanDNA-b19450/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:00,816] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:00,816] [INFO] Task started: HMMsearch
[2023-03-15 09:00:00,816] [INFO] Running command: hmmsearch --tblout OceanDNA-b19450/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a973595-cd24-43ca-8620-90883a3a121c/dqc_reference/reference_markers.hmm OceanDNA-b19450/protein.faa > /dev/null
[2023-03-15 09:00:01,012] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:01,013] [INFO] Found 6/6 markers.
[2023-03-15 09:00:01,028] [INFO] Query marker FASTA was written to OceanDNA-b19450/markers.fasta
[2023-03-15 09:00:01,028] [INFO] Task started: Blastn
[2023-03-15 09:00:01,028] [INFO] Running command: blastn -query OceanDNA-b19450/markers.fasta -db /var/lib/cwl/stg9a973595-cd24-43ca-8620-90883a3a121c/dqc_reference/reference_markers.fasta -out OceanDNA-b19450/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:01,565] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:01,566] [INFO] Selected 14 target genomes.
[2023-03-15 09:00:01,567] [INFO] Target genome list was writen to OceanDNA-b19450/target_genomes.txt
[2023-03-15 09:00:01,577] [INFO] Task started: fastANI
[2023-03-15 09:00:01,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f84621c-0b5f-4c7b-97b4-e5e6f8e4280d/OceanDNA-b19450.fa --refList OceanDNA-b19450/target_genomes.txt --output OceanDNA-b19450/fastani_result.tsv --threads 1
[2023-03-15 09:00:09,500] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:09,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a973595-cd24-43ca-8620-90883a3a121c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:09,501] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a973595-cd24-43ca-8620-90883a3a121c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:09,501] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:09,501] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:00:09,501] [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 09:00:09,501] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19450/tc_result.tsv
[2023-03-15 09:00:09,501] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:09,501] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:09,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a973595-cd24-43ca-8620-90883a3a121c/dqc_reference/checkm_data
[2023-03-15 09:00:09,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:09,508] [INFO] Task started: CheckM
[2023-03-15 09:00:09,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19450/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19450/checkm_input OceanDNA-b19450/checkm_result
[2023-03-15 09:00:40,843] [INFO] Task succeeded: CheckM
[2023-03-15 09:00:40,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:00:40,845] [INFO] ===== Completeness check finished =====
[2023-03-15 09:00:40,845] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:00:40,846] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19450/markers.fasta)
[2023-03-15 09:00:40,846] [INFO] Task started: Blastn
[2023-03-15 09:00:40,846] [INFO] Running command: blastn -query OceanDNA-b19450/markers.fasta -db /var/lib/cwl/stg9a973595-cd24-43ca-8620-90883a3a121c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19450/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:41,555] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:41,556] [INFO] Selected 23 target genomes.
[2023-03-15 09:00:41,556] [INFO] Target genome list was writen to OceanDNA-b19450/target_genomes_gtdb.txt
[2023-03-15 09:00:41,590] [INFO] Task started: fastANI
[2023-03-15 09:00:41,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f84621c-0b5f-4c7b-97b4-e5e6f8e4280d/OceanDNA-b19450.fa --refList OceanDNA-b19450/target_genomes_gtdb.txt --output OceanDNA-b19450/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:00:53,434] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:53,436] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:00:53,436] [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_002256485.1	s__UBA2126 sp002256485	78.7757	139	600	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004124385.1	s__UBA2126 sp004124385	76.6332	115	600	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	99.49	99.49	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:00:53,437] [INFO] GTDB search result was written to OceanDNA-b19450/result_gtdb.tsv
[2023-03-15 09:00:53,437] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:00:53,437] [INFO] DFAST_QC result json was written to OceanDNA-b19450/dqc_result.json
[2023-03-15 09:00:53,437] [INFO] DFAST_QC completed!
[2023-03-15 09:00:53,437] [INFO] Total running time: 0h1m4s