[2023-03-17 03:24:50,921] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:24:50,921] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:24:50,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c168c65-b8b5-4fd7-86de-e56463b868e6/dqc_reference
[2023-03-17 03:24:52,053] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:24:52,053] [INFO] Task started: Prodigal
[2023-03-17 03:24:52,053] [INFO] Running command: cat /var/lib/cwl/stg74a3dd63-c4ae-4e3d-aaa3-040adfed81e2/OceanDNA-b515.fa | prodigal -d OceanDNA-b515/cds.fna -a OceanDNA-b515/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:24:59,626] [INFO] Task succeeded: Prodigal
[2023-03-17 03:24:59,626] [INFO] Task started: HMMsearch
[2023-03-17 03:24:59,626] [INFO] Running command: hmmsearch --tblout OceanDNA-b515/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c168c65-b8b5-4fd7-86de-e56463b868e6/dqc_reference/reference_markers.hmm OceanDNA-b515/protein.faa > /dev/null
[2023-03-17 03:24:59,775] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:24:59,775] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg74a3dd63-c4ae-4e3d-aaa3-040adfed81e2/OceanDNA-b515.fa]
[2023-03-17 03:24:59,793] [INFO] Query marker FASTA was written to OceanDNA-b515/markers.fasta
[2023-03-17 03:24:59,794] [INFO] Task started: Blastn
[2023-03-17 03:24:59,794] [INFO] Running command: blastn -query OceanDNA-b515/markers.fasta -db /var/lib/cwl/stg6c168c65-b8b5-4fd7-86de-e56463b868e6/dqc_reference/reference_markers.fasta -out OceanDNA-b515/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:00,324] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:00,325] [INFO] Selected 11 target genomes.
[2023-03-17 03:25:00,325] [INFO] Target genome list was writen to OceanDNA-b515/target_genomes.txt
[2023-03-17 03:25:00,331] [INFO] Task started: fastANI
[2023-03-17 03:25:00,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a3dd63-c4ae-4e3d-aaa3-040adfed81e2/OceanDNA-b515.fa --refList OceanDNA-b515/target_genomes.txt --output OceanDNA-b515/fastani_result.tsv --threads 1
[2023-03-17 03:25:09,229] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:09,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c168c65-b8b5-4fd7-86de-e56463b868e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:25:09,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c168c65-b8b5-4fd7-86de-e56463b868e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:25:09,233] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:25:09,233] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:25:09,233] [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
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	78.6354	75	143	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.2636	53	143	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:25:09,233] [INFO] DFAST Taxonomy check result was written to OceanDNA-b515/tc_result.tsv
[2023-03-17 03:25:09,234] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:25:09,234] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:25:09,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c168c65-b8b5-4fd7-86de-e56463b868e6/dqc_reference/checkm_data
[2023-03-17 03:25:09,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:25:09,238] [INFO] Task started: CheckM
[2023-03-17 03:25:09,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b515/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b515/checkm_input OceanDNA-b515/checkm_result
[2023-03-17 03:25:33,133] [INFO] Task succeeded: CheckM
[2023-03-17 03:25:33,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:25:33,157] [INFO] ===== Completeness check finished =====
[2023-03-17 03:25:33,157] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:25:33,157] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b515/markers.fasta)
[2023-03-17 03:25:33,158] [INFO] Task started: Blastn
[2023-03-17 03:25:33,158] [INFO] Running command: blastn -query OceanDNA-b515/markers.fasta -db /var/lib/cwl/stg6c168c65-b8b5-4fd7-86de-e56463b868e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b515/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:33,864] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:33,869] [INFO] Selected 13 target genomes.
[2023-03-17 03:25:33,869] [INFO] Target genome list was writen to OceanDNA-b515/target_genomes_gtdb.txt
[2023-03-17 03:25:33,918] [INFO] Task started: fastANI
[2023-03-17 03:25:33,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a3dd63-c4ae-4e3d-aaa3-040adfed81e2/OceanDNA-b515.fa --refList OceanDNA-b515/target_genomes_gtdb.txt --output OceanDNA-b515/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:25:42,158] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:42,161] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:25:42,161] [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_002698945.1	s__Ilumatobacter sp002698945	78.7697	69	143	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	78.5819	76	143	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	76.794	52	143	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	76.2636	53	143	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:25:42,163] [INFO] GTDB search result was written to OceanDNA-b515/result_gtdb.tsv
[2023-03-17 03:25:42,163] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:25:42,164] [INFO] DFAST_QC result json was written to OceanDNA-b515/dqc_result.json
[2023-03-17 03:25:42,164] [INFO] DFAST_QC completed!
[2023-03-17 03:25:42,164] [INFO] Total running time: 0h0m51s