[2023-03-19 01:26:02,193] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:26:02,193] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:26:02,193] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb86c261-8f00-45ab-b362-a4a532fec3bb/dqc_reference
[2023-03-19 01:26:03,786] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:26:03,787] [INFO] Task started: Prodigal
[2023-03-19 01:26:03,787] [INFO] Running command: cat /var/lib/cwl/stgabedfacf-9307-4930-944a-4878c707bbc8/OceanDNA-b20416.fa | prodigal -d OceanDNA-b20416/cds.fna -a OceanDNA-b20416/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:26:07,126] [INFO] Task succeeded: Prodigal
[2023-03-19 01:26:07,126] [INFO] Task started: HMMsearch
[2023-03-19 01:26:07,126] [INFO] Running command: hmmsearch --tblout OceanDNA-b20416/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb86c261-8f00-45ab-b362-a4a532fec3bb/dqc_reference/reference_markers.hmm OceanDNA-b20416/protein.faa > /dev/null
[2023-03-19 01:26:07,273] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:26:07,273] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgabedfacf-9307-4930-944a-4878c707bbc8/OceanDNA-b20416.fa]
[2023-03-19 01:26:07,283] [INFO] Query marker FASTA was written to OceanDNA-b20416/markers.fasta
[2023-03-19 01:26:07,285] [INFO] Task started: Blastn
[2023-03-19 01:26:07,285] [INFO] Running command: blastn -query OceanDNA-b20416/markers.fasta -db /var/lib/cwl/stgeb86c261-8f00-45ab-b362-a4a532fec3bb/dqc_reference/reference_markers.fasta -out OceanDNA-b20416/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:26:07,995] [INFO] Task succeeded: Blastn
[2023-03-19 01:26:07,996] [INFO] Selected 11 target genomes.
[2023-03-19 01:26:07,996] [INFO] Target genome list was writen to OceanDNA-b20416/target_genomes.txt
[2023-03-19 01:26:08,004] [INFO] Task started: fastANI
[2023-03-19 01:26:08,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgabedfacf-9307-4930-944a-4878c707bbc8/OceanDNA-b20416.fa --refList OceanDNA-b20416/target_genomes.txt --output OceanDNA-b20416/fastani_result.tsv --threads 1
[2023-03-19 01:26:14,041] [INFO] Task succeeded: fastANI
[2023-03-19 01:26:14,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb86c261-8f00-45ab-b362-a4a532fec3bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:26:14,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb86c261-8f00-45ab-b362-a4a532fec3bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:26:14,042] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:26:14,042] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:26:14,042] [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
--------------------------------------------------------------------------------
[2023-03-19 01:26:14,043] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20416/tc_result.tsv
[2023-03-19 01:26:14,043] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:26:14,043] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:26:14,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb86c261-8f00-45ab-b362-a4a532fec3bb/dqc_reference/checkm_data
[2023-03-19 01:26:14,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:26:14,101] [INFO] Task started: CheckM
[2023-03-19 01:26:14,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20416/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20416/checkm_input OceanDNA-b20416/checkm_result
[2023-03-19 01:26:29,163] [INFO] Task succeeded: CheckM
[2023-03-19 01:26:29,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:26:29,165] [INFO] ===== Completeness check finished =====
[2023-03-19 01:26:29,165] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:26:29,166] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20416/markers.fasta)
[2023-03-19 01:26:29,167] [INFO] Task started: Blastn
[2023-03-19 01:26:29,167] [INFO] Running command: blastn -query OceanDNA-b20416/markers.fasta -db /var/lib/cwl/stgeb86c261-8f00-45ab-b362-a4a532fec3bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20416/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:26:30,137] [INFO] Task succeeded: Blastn
[2023-03-19 01:26:30,138] [INFO] Selected 21 target genomes.
[2023-03-19 01:26:30,138] [INFO] Target genome list was writen to OceanDNA-b20416/target_genomes_gtdb.txt
[2023-03-19 01:26:30,169] [INFO] Task started: fastANI
[2023-03-19 01:26:30,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgabedfacf-9307-4930-944a-4878c707bbc8/OceanDNA-b20416.fa --refList OceanDNA-b20416/target_genomes_gtdb.txt --output OceanDNA-b20416/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:26:39,679] [INFO] Task succeeded: fastANI
[2023-03-19 01:26:39,681] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:26:39,682] [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_004124405.1	s__D37C17 sp004124405	78.1544	96	205	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__D37C17;g__D37C17	95.0	97.83	97.40	0.76	0.68	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:26:39,682] [INFO] GTDB search result was written to OceanDNA-b20416/result_gtdb.tsv
[2023-03-19 01:26:39,682] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:26:39,683] [INFO] DFAST_QC result json was written to OceanDNA-b20416/dqc_result.json
[2023-03-19 01:26:39,683] [INFO] DFAST_QC completed!
[2023-03-19 01:26:39,683] [INFO] Total running time: 0h0m37s