[2023-03-17 10:56:24,891] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:56:24,891] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:56:24,891] [INFO] DQC Reference Directory: /var/lib/cwl/stgec702c17-4a3e-4e46-a354-4e90c87a7acc/dqc_reference
[2023-03-17 10:56:29,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:56:29,190] [INFO] Task started: Prodigal
[2023-03-17 10:56:29,190] [INFO] Running command: cat /var/lib/cwl/stgd2bb8084-f945-4351-9258-3f267555e7e5/OceanDNA-b4053.fa | prodigal -d OceanDNA-b4053/cds.fna -a OceanDNA-b4053/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:56:45,034] [INFO] Task succeeded: Prodigal
[2023-03-17 10:56:45,035] [INFO] Task started: HMMsearch
[2023-03-17 10:56:45,035] [INFO] Running command: hmmsearch --tblout OceanDNA-b4053/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec702c17-4a3e-4e46-a354-4e90c87a7acc/dqc_reference/reference_markers.hmm OceanDNA-b4053/protein.faa > /dev/null
[2023-03-17 10:56:45,287] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:56:45,288] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd2bb8084-f945-4351-9258-3f267555e7e5/OceanDNA-b4053.fa]
[2023-03-17 10:56:45,308] [INFO] Query marker FASTA was written to OceanDNA-b4053/markers.fasta
[2023-03-17 10:56:45,309] [INFO] Task started: Blastn
[2023-03-17 10:56:45,309] [INFO] Running command: blastn -query OceanDNA-b4053/markers.fasta -db /var/lib/cwl/stgec702c17-4a3e-4e46-a354-4e90c87a7acc/dqc_reference/reference_markers.fasta -out OceanDNA-b4053/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:56:48,747] [INFO] Task succeeded: Blastn
[2023-03-17 10:56:48,747] [INFO] Selected 26 target genomes.
[2023-03-17 10:56:48,748] [INFO] Target genome list was writen to OceanDNA-b4053/target_genomes.txt
[2023-03-17 10:56:48,877] [INFO] Task started: fastANI
[2023-03-17 10:56:48,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2bb8084-f945-4351-9258-3f267555e7e5/OceanDNA-b4053.fa --refList OceanDNA-b4053/target_genomes.txt --output OceanDNA-b4053/fastani_result.tsv --threads 1
[2023-03-17 10:57:07,496] [INFO] Task succeeded: fastANI
[2023-03-17 10:57:07,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec702c17-4a3e-4e46-a354-4e90c87a7acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:57:07,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec702c17-4a3e-4e46-a354-4e90c87a7acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:57:07,581] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:57:07,581] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:57:07,581] [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
Ekhidna lutea	strain=DSM 19307	GCA_900188325.1	447679	447679	type	True	83.7049	339	621	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:57:07,581] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4053/tc_result.tsv
[2023-03-17 10:57:07,581] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:57:07,581] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:57:07,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec702c17-4a3e-4e46-a354-4e90c87a7acc/dqc_reference/checkm_data
[2023-03-17 10:57:07,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:57:07,595] [INFO] Task started: CheckM
[2023-03-17 10:57:07,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4053/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4053/checkm_input OceanDNA-b4053/checkm_result
[2023-03-17 10:57:52,994] [INFO] Task succeeded: CheckM
[2023-03-17 10:57:52,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:57:52,997] [INFO] ===== Completeness check finished =====
[2023-03-17 10:57:52,997] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:57:52,997] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4053/markers.fasta)
[2023-03-17 10:57:52,998] [INFO] Task started: Blastn
[2023-03-17 10:57:52,998] [INFO] Running command: blastn -query OceanDNA-b4053/markers.fasta -db /var/lib/cwl/stgec702c17-4a3e-4e46-a354-4e90c87a7acc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4053/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:57:54,018] [INFO] Task succeeded: Blastn
[2023-03-17 10:57:54,084] [INFO] Selected 31 target genomes.
[2023-03-17 10:57:54,084] [INFO] Target genome list was writen to OceanDNA-b4053/target_genomes_gtdb.txt
[2023-03-17 10:57:54,513] [INFO] Task started: fastANI
[2023-03-17 10:57:54,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2bb8084-f945-4351-9258-3f267555e7e5/OceanDNA-b4053.fa --refList OceanDNA-b4053/target_genomes_gtdb.txt --output OceanDNA-b4053/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:58:15,389] [INFO] Task succeeded: fastANI
[2023-03-17 10:58:15,393] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:58:15,393] [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
GCF_900188325.1	s__Ekhidna lutea	83.7106	339	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ekhidna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006969745.1	s__Ekhidna sp006969745	77.7437	158	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ekhidna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214445.1	s__Ekhidna sp013214445	77.0362	53	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ekhidna	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:58:15,393] [INFO] GTDB search result was written to OceanDNA-b4053/result_gtdb.tsv
[2023-03-17 10:58:15,393] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:58:15,394] [INFO] DFAST_QC result json was written to OceanDNA-b4053/dqc_result.json
[2023-03-17 10:58:15,394] [INFO] DFAST_QC completed!
[2023-03-17 10:58:15,394] [INFO] Total running time: 0h1m51s