[2023-03-17 05:10:04,854] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:10:04,854] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:10:04,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e52e1f3-a10a-4c0b-bca4-6434f3b65e45/dqc_reference
[2023-03-17 05:10:05,995] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:10:05,995] [INFO] Task started: Prodigal
[2023-03-17 05:10:05,996] [INFO] Running command: cat /var/lib/cwl/stg104f39c0-2a7c-4eb5-92b4-b54b31cb2d1c/OceanDNA-b43053.fa | prodigal -d OceanDNA-b43053/cds.fna -a OceanDNA-b43053/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:10:08,818] [INFO] Task succeeded: Prodigal
[2023-03-17 05:10:08,818] [INFO] Task started: HMMsearch
[2023-03-17 05:10:08,819] [INFO] Running command: hmmsearch --tblout OceanDNA-b43053/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e52e1f3-a10a-4c0b-bca4-6434f3b65e45/dqc_reference/reference_markers.hmm OceanDNA-b43053/protein.faa > /dev/null
[2023-03-17 05:10:08,956] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:10:08,957] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg104f39c0-2a7c-4eb5-92b4-b54b31cb2d1c/OceanDNA-b43053.fa]
[2023-03-17 05:10:08,963] [INFO] Query marker FASTA was written to OceanDNA-b43053/markers.fasta
[2023-03-17 05:10:08,964] [INFO] Task started: Blastn
[2023-03-17 05:10:08,964] [INFO] Running command: blastn -query OceanDNA-b43053/markers.fasta -db /var/lib/cwl/stg5e52e1f3-a10a-4c0b-bca4-6434f3b65e45/dqc_reference/reference_markers.fasta -out OceanDNA-b43053/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:09,668] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:09,668] [INFO] Selected 5 target genomes.
[2023-03-17 05:10:09,669] [INFO] Target genome list was writen to OceanDNA-b43053/target_genomes.txt
[2023-03-17 05:10:09,674] [INFO] Task started: fastANI
[2023-03-17 05:10:09,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg104f39c0-2a7c-4eb5-92b4-b54b31cb2d1c/OceanDNA-b43053.fa --refList OceanDNA-b43053/target_genomes.txt --output OceanDNA-b43053/fastani_result.tsv --threads 1
[2023-03-17 05:10:12,264] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:12,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e52e1f3-a10a-4c0b-bca4-6434f3b65e45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:10:12,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e52e1f3-a10a-4c0b-bca4-6434f3b65e45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:10:12,320] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:10:12,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:10:12,321] [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
Candidatus Pseudothioglobus singularis	strain=PS1	GCA_001281385.1	1427364	1427364	type	True	85.2131	146	168	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:10:12,321] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43053/tc_result.tsv
[2023-03-17 05:10:12,321] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:10:12,321] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:10:12,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e52e1f3-a10a-4c0b-bca4-6434f3b65e45/dqc_reference/checkm_data
[2023-03-17 05:10:12,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:10:12,901] [INFO] Task started: CheckM
[2023-03-17 05:10:12,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43053/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43053/checkm_input OceanDNA-b43053/checkm_result
[2023-03-17 05:10:31,299] [INFO] Task succeeded: CheckM
[2023-03-17 05:10:31,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:10:31,301] [INFO] ===== Completeness check finished =====
[2023-03-17 05:10:31,301] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:10:31,301] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43053/markers.fasta)
[2023-03-17 05:10:31,302] [INFO] Task started: Blastn
[2023-03-17 05:10:31,302] [INFO] Running command: blastn -query OceanDNA-b43053/markers.fasta -db /var/lib/cwl/stg5e52e1f3-a10a-4c0b-bca4-6434f3b65e45/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43053/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:32,183] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:32,184] [INFO] Selected 5 target genomes.
[2023-03-17 05:10:32,184] [INFO] Target genome list was writen to OceanDNA-b43053/target_genomes_gtdb.txt
[2023-03-17 05:10:32,272] [INFO] Task started: fastANI
[2023-03-17 05:10:32,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg104f39c0-2a7c-4eb5-92b4-b54b31cb2d1c/OceanDNA-b43053.fa --refList OceanDNA-b43053/target_genomes_gtdb.txt --output OceanDNA-b43053/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:10:34,164] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:34,167] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:10:34,167] [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_902513495.1	s__Pseudothioglobus sp902513495	86.1785	91	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.65	97.05	0.53	0.51	3	-
GCF_001281385.1	s__Pseudothioglobus singularis	85.2131	146	168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	95.87	0.84	0.66	7	-
--------------------------------------------------------------------------------
[2023-03-17 05:10:34,167] [INFO] GTDB search result was written to OceanDNA-b43053/result_gtdb.tsv
[2023-03-17 05:10:34,167] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:10:34,168] [INFO] DFAST_QC result json was written to OceanDNA-b43053/dqc_result.json
[2023-03-17 05:10:34,168] [INFO] DFAST_QC completed!
[2023-03-17 05:10:34,168] [INFO] Total running time: 0h0m29s