[2023-03-15 09:48:16,399] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,400] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e13f5fa-30e8-4fe8-a555-8315b9888464/dqc_reference
[2023-03-15 09:48:18,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,054] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,054] [INFO] Running command: cat /var/lib/cwl/stgadf09fd0-0c00-4cc2-8ed1-3d97545bf784/OceanDNA-a4235.fa | prodigal -d OceanDNA-a4235/cds.fna -a OceanDNA-a4235/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:22,687] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:22,687] [INFO] Task started: HMMsearch
[2023-03-15 09:48:22,687] [INFO] Running command: hmmsearch --tblout OceanDNA-a4235/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e13f5fa-30e8-4fe8-a555-8315b9888464/dqc_reference/reference_markers.hmm OceanDNA-a4235/protein.faa > /dev/null
[2023-03-15 09:48:22,844] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:22,844] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgadf09fd0-0c00-4cc2-8ed1-3d97545bf784/OceanDNA-a4235.fa]
[2023-03-15 09:48:22,854] [INFO] Query marker FASTA was written to OceanDNA-a4235/markers.fasta
[2023-03-15 09:48:22,854] [INFO] Task started: Blastn
[2023-03-15 09:48:22,854] [INFO] Running command: blastn -query OceanDNA-a4235/markers.fasta -db /var/lib/cwl/stg1e13f5fa-30e8-4fe8-a555-8315b9888464/dqc_reference/reference_markers.fasta -out OceanDNA-a4235/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:24,955] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:24,956] [INFO] Selected 6 target genomes.
[2023-03-15 09:48:24,956] [INFO] Target genome list was writen to OceanDNA-a4235/target_genomes.txt
[2023-03-15 09:48:24,961] [INFO] Task started: fastANI
[2023-03-15 09:48:24,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf09fd0-0c00-4cc2-8ed1-3d97545bf784/OceanDNA-a4235.fa --refList OceanDNA-a4235/target_genomes.txt --output OceanDNA-a4235/fastani_result.tsv --threads 1
[2023-03-15 09:48:26,608] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:26,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e13f5fa-30e8-4fe8-a555-8315b9888464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:26,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e13f5fa-30e8-4fe8-a555-8315b9888464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:26,609] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:26,609] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:26,609] [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 09:48:26,609] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4235/tc_result.tsv
[2023-03-15 09:48:26,609] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:26,610] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:26,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e13f5fa-30e8-4fe8-a555-8315b9888464/dqc_reference/checkm_data
[2023-03-15 09:48:26,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:26,615] [INFO] Task started: CheckM
[2023-03-15 09:48:26,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4235/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4235/checkm_input OceanDNA-a4235/checkm_result
[2023-03-15 09:48:50,301] [INFO] Task succeeded: CheckM
[2023-03-15 09:48:50,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.79%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 09:48:50,303] [INFO] ===== Completeness check finished =====
[2023-03-15 09:48:50,303] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:48:50,303] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4235/markers.fasta)
[2023-03-15 09:48:50,303] [INFO] Task started: Blastn
[2023-03-15 09:48:50,303] [INFO] Running command: blastn -query OceanDNA-a4235/markers.fasta -db /var/lib/cwl/stg1e13f5fa-30e8-4fe8-a555-8315b9888464/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4235/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:51,731] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:51,732] [INFO] Selected 10 target genomes.
[2023-03-15 09:48:51,732] [INFO] Target genome list was writen to OceanDNA-a4235/target_genomes_gtdb.txt
[2023-03-15 09:48:51,912] [INFO] Task started: fastANI
[2023-03-15 09:48:51,912] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf09fd0-0c00-4cc2-8ed1-3d97545bf784/OceanDNA-a4235.fa --refList OceanDNA-a4235/target_genomes_gtdb.txt --output OceanDNA-a4235/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:48:54,547] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:54,550] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:48:54,550] [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_001629205.1	s__MGIIb-O3 sp001629205	95.2212	235	272	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002496485.1	s__MGIIb-O3 sp002496485	84.0401	209	272	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.23	98.23	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:48:54,550] [INFO] GTDB search result was written to OceanDNA-a4235/result_gtdb.tsv
[2023-03-15 09:48:54,550] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:48:54,551] [INFO] DFAST_QC result json was written to OceanDNA-a4235/dqc_result.json
[2023-03-15 09:48:54,551] [INFO] DFAST_QC completed!
[2023-03-15 09:48:54,551] [INFO] Total running time: 0h0m38s