[2023-03-16 18:40:20,526] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:40:20,526] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:40:20,526] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7a3d072-8a47-4124-91de-6125656d3fb2/dqc_reference
[2023-03-16 18:40:22,806] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:40:22,807] [INFO] Task started: Prodigal
[2023-03-16 18:40:22,807] [INFO] Running command: cat /var/lib/cwl/stgc69f4d64-7119-461a-b738-bce229c809e9/OceanDNA-b33859.fa | prodigal -d OceanDNA-b33859/cds.fna -a OceanDNA-b33859/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:40:28,002] [INFO] Task succeeded: Prodigal
[2023-03-16 18:40:28,002] [INFO] Task started: HMMsearch
[2023-03-16 18:40:28,002] [INFO] Running command: hmmsearch --tblout OceanDNA-b33859/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7a3d072-8a47-4124-91de-6125656d3fb2/dqc_reference/reference_markers.hmm OceanDNA-b33859/protein.faa > /dev/null
[2023-03-16 18:40:28,228] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:40:28,229] [INFO] Found 6/6 markers.
[2023-03-16 18:40:28,237] [INFO] Query marker FASTA was written to OceanDNA-b33859/markers.fasta
[2023-03-16 18:40:28,239] [INFO] Task started: Blastn
[2023-03-16 18:40:28,239] [INFO] Running command: blastn -query OceanDNA-b33859/markers.fasta -db /var/lib/cwl/stgf7a3d072-8a47-4124-91de-6125656d3fb2/dqc_reference/reference_markers.fasta -out OceanDNA-b33859/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:40:31,180] [INFO] Task succeeded: Blastn
[2023-03-16 18:40:31,181] [INFO] Selected 22 target genomes.
[2023-03-16 18:40:31,182] [INFO] Target genome list was writen to OceanDNA-b33859/target_genomes.txt
[2023-03-16 18:40:31,199] [INFO] Task started: fastANI
[2023-03-16 18:40:31,199] [INFO] Running command: fastANI --query /var/lib/cwl/stgc69f4d64-7119-461a-b738-bce229c809e9/OceanDNA-b33859.fa --refList OceanDNA-b33859/target_genomes.txt --output OceanDNA-b33859/fastani_result.tsv --threads 1
[2023-03-16 18:40:52,862] [INFO] Task succeeded: fastANI
[2023-03-16 18:40:52,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7a3d072-8a47-4124-91de-6125656d3fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:40:52,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7a3d072-8a47-4124-91de-6125656d3fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:40:52,863] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:40:52,863] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:40:52,863] [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
--------------------------------------------------------------------------------
[2023-03-16 18:40:52,863] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33859/tc_result.tsv
[2023-03-16 18:40:52,863] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:40:52,864] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:40:52,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7a3d072-8a47-4124-91de-6125656d3fb2/dqc_reference/checkm_data
[2023-03-16 18:40:52,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:40:53,028] [INFO] Task started: CheckM
[2023-03-16 18:40:53,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33859/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33859/checkm_input OceanDNA-b33859/checkm_result
[2023-03-16 18:41:15,495] [INFO] Task succeeded: CheckM
[2023-03-16 18:41:15,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:41:15,497] [INFO] ===== Completeness check finished =====
[2023-03-16 18:41:15,497] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:41:15,497] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33859/markers.fasta)
[2023-03-16 18:41:15,498] [INFO] Task started: Blastn
[2023-03-16 18:41:15,498] [INFO] Running command: blastn -query OceanDNA-b33859/markers.fasta -db /var/lib/cwl/stgf7a3d072-8a47-4124-91de-6125656d3fb2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33859/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:41:16,388] [INFO] Task succeeded: Blastn
[2023-03-16 18:41:16,388] [INFO] Selected 16 target genomes.
[2023-03-16 18:41:16,389] [INFO] Target genome list was writen to OceanDNA-b33859/target_genomes_gtdb.txt
[2023-03-16 18:41:16,581] [INFO] Task started: fastANI
[2023-03-16 18:41:16,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgc69f4d64-7119-461a-b738-bce229c809e9/OceanDNA-b33859.fa --refList OceanDNA-b33859/target_genomes_gtdb.txt --output OceanDNA-b33859/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:41:20,536] [INFO] Task succeeded: fastANI
[2023-03-16 18:41:20,540] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:41:20,540] [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_018657165.1	s__BACL14 sp018657165	99.2609	241	337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.24	99.09	0.82	0.76	15	conclusive
GCA_905181685.1	s__BACL14 sp905181685	81.1019	171	337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607785.1	s__BACL14 sp018607785	80.222	235	337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.17	98.94	0.86	0.81	5	-
--------------------------------------------------------------------------------
[2023-03-16 18:41:20,540] [INFO] GTDB search result was written to OceanDNA-b33859/result_gtdb.tsv
[2023-03-16 18:41:20,540] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:41:20,541] [INFO] DFAST_QC result json was written to OceanDNA-b33859/dqc_result.json
[2023-03-16 18:41:20,541] [INFO] DFAST_QC completed!
[2023-03-16 18:41:20,541] [INFO] Total running time: 0h1m0s