[2023-03-17 06:30:49,799] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,799] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,799] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5feec65-71b1-4413-b795-69ee71f28f97/dqc_reference
[2023-03-17 06:30:51,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:51,360] [INFO] Task started: Prodigal
[2023-03-17 06:30:51,360] [INFO] Running command: cat /var/lib/cwl/stg699e3d03-db11-4194-a048-e2d3ba227f5d/OceanDNA-b33789.fa | prodigal -d OceanDNA-b33789/cds.fna -a OceanDNA-b33789/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:30:54,352] [INFO] Task succeeded: Prodigal
[2023-03-17 06:30:54,352] [INFO] Task started: HMMsearch
[2023-03-17 06:30:54,352] [INFO] Running command: hmmsearch --tblout OceanDNA-b33789/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5feec65-71b1-4413-b795-69ee71f28f97/dqc_reference/reference_markers.hmm OceanDNA-b33789/protein.faa > /dev/null
[2023-03-17 06:30:54,546] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:30:54,547] [INFO] Found 6/6 markers.
[2023-03-17 06:30:54,554] [INFO] Query marker FASTA was written to OceanDNA-b33789/markers.fasta
[2023-03-17 06:30:54,556] [INFO] Task started: Blastn
[2023-03-17 06:30:54,557] [INFO] Running command: blastn -query OceanDNA-b33789/markers.fasta -db /var/lib/cwl/stgd5feec65-71b1-4413-b795-69ee71f28f97/dqc_reference/reference_markers.fasta -out OceanDNA-b33789/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:30:57,045] [INFO] Task succeeded: Blastn
[2023-03-17 06:30:57,046] [INFO] Selected 21 target genomes.
[2023-03-17 06:30:57,046] [INFO] Target genome list was writen to OceanDNA-b33789/target_genomes.txt
[2023-03-17 06:30:57,057] [INFO] Task started: fastANI
[2023-03-17 06:30:57,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg699e3d03-db11-4194-a048-e2d3ba227f5d/OceanDNA-b33789.fa --refList OceanDNA-b33789/target_genomes.txt --output OceanDNA-b33789/fastani_result.tsv --threads 1
[2023-03-17 06:31:05,537] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:05,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5feec65-71b1-4413-b795-69ee71f28f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:05,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5feec65-71b1-4413-b795-69ee71f28f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:05,538] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:05,538] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:05,538] [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
--------------------------------------------------------------------------------
[2023-03-17 06:31:05,538] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33789/tc_result.tsv
[2023-03-17 06:31:05,538] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:05,539] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:05,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5feec65-71b1-4413-b795-69ee71f28f97/dqc_reference/checkm_data
[2023-03-17 06:31:05,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:05,543] [INFO] Task started: CheckM
[2023-03-17 06:31:05,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33789/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33789/checkm_input OceanDNA-b33789/checkm_result
[2023-03-17 06:31:20,684] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:20,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:20,686] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:20,686] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:20,686] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33789/markers.fasta)
[2023-03-17 06:31:20,688] [INFO] Task started: Blastn
[2023-03-17 06:31:20,689] [INFO] Running command: blastn -query OceanDNA-b33789/markers.fasta -db /var/lib/cwl/stgd5feec65-71b1-4413-b795-69ee71f28f97/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33789/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:21,541] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:21,542] [INFO] Selected 19 target genomes.
[2023-03-17 06:31:21,542] [INFO] Target genome list was writen to OceanDNA-b33789/target_genomes_gtdb.txt
[2023-03-17 06:31:22,158] [INFO] Task started: fastANI
[2023-03-17 06:31:22,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg699e3d03-db11-4194-a048-e2d3ba227f5d/OceanDNA-b33789.fa --refList OceanDNA-b33789/target_genomes_gtdb.txt --output OceanDNA-b33789/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:31:27,011] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:27,015] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:31:27,015] [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_905181685.1	s__BACL14 sp905181685	96.3973	125	173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018607785.1	s__BACL14 sp018607785	80.0329	130	173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.17	98.94	0.86	0.81	5	-
GCA_018657165.1	s__BACL14 sp018657165	79.7582	114	173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.24	99.09	0.82	0.76	15	-
GCA_905182075.1	s__BACL14 sp905182075	77.9673	58	173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:31:27,015] [INFO] GTDB search result was written to OceanDNA-b33789/result_gtdb.tsv
[2023-03-17 06:31:27,015] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:31:27,016] [INFO] DFAST_QC result json was written to OceanDNA-b33789/dqc_result.json
[2023-03-17 06:31:27,016] [INFO] DFAST_QC completed!
[2023-03-17 06:31:27,016] [INFO] Total running time: 0h0m37s