[2023-03-18 03:45:10,276] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,276] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e6ea33e-2b9b-42c1-915e-924ecbe7b365/dqc_reference
[2023-03-18 03:45:12,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,145] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,145] [INFO] Running command: cat /var/lib/cwl/stga7ee9f73-0ddb-4fbb-9177-bd04825dfd71/OceanDNA-b35629.fa | prodigal -d OceanDNA-b35629/cds.fna -a OceanDNA-b35629/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:14,801] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:14,801] [INFO] Task started: HMMsearch
[2023-03-18 03:45:14,801] [INFO] Running command: hmmsearch --tblout OceanDNA-b35629/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e6ea33e-2b9b-42c1-915e-924ecbe7b365/dqc_reference/reference_markers.hmm OceanDNA-b35629/protein.faa > /dev/null
[2023-03-18 03:45:15,048] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:15,048] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga7ee9f73-0ddb-4fbb-9177-bd04825dfd71/OceanDNA-b35629.fa]
[2023-03-18 03:45:15,054] [INFO] Query marker FASTA was written to OceanDNA-b35629/markers.fasta
[2023-03-18 03:45:15,056] [INFO] Task started: Blastn
[2023-03-18 03:45:15,056] [INFO] Running command: blastn -query OceanDNA-b35629/markers.fasta -db /var/lib/cwl/stg3e6ea33e-2b9b-42c1-915e-924ecbe7b365/dqc_reference/reference_markers.fasta -out OceanDNA-b35629/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:17,823] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:17,824] [INFO] Selected 13 target genomes.
[2023-03-18 03:45:17,824] [INFO] Target genome list was writen to OceanDNA-b35629/target_genomes.txt
[2023-03-18 03:45:17,832] [INFO] Task started: fastANI
[2023-03-18 03:45:17,832] [INFO] Running command: fastANI --query /var/lib/cwl/stga7ee9f73-0ddb-4fbb-9177-bd04825dfd71/OceanDNA-b35629.fa --refList OceanDNA-b35629/target_genomes.txt --output OceanDNA-b35629/fastani_result.tsv --threads 1
[2023-03-18 03:45:22,681] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:22,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e6ea33e-2b9b-42c1-915e-924ecbe7b365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:22,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e6ea33e-2b9b-42c1-915e-924ecbe7b365/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:22,682] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:22,682] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:45:22,682] [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
--------------------------------------------------------------------------------
[2023-03-18 03:45:22,682] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35629/tc_result.tsv
[2023-03-18 03:45:22,682] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:22,683] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:22,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e6ea33e-2b9b-42c1-915e-924ecbe7b365/dqc_reference/checkm_data
[2023-03-18 03:45:22,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:22,688] [INFO] Task started: CheckM
[2023-03-18 03:45:22,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35629/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35629/checkm_input OceanDNA-b35629/checkm_result
[2023-03-18 03:45:39,016] [INFO] Task succeeded: CheckM
[2023-03-18 03:45:39,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.68%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 03:45:39,018] [INFO] ===== Completeness check finished =====
[2023-03-18 03:45:39,018] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:45:39,018] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35629/markers.fasta)
[2023-03-18 03:45:39,020] [INFO] Task started: Blastn
[2023-03-18 03:45:39,020] [INFO] Running command: blastn -query OceanDNA-b35629/markers.fasta -db /var/lib/cwl/stg3e6ea33e-2b9b-42c1-915e-924ecbe7b365/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35629/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:40,237] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:40,238] [INFO] Selected 27 target genomes.
[2023-03-18 03:45:40,238] [INFO] Target genome list was writen to OceanDNA-b35629/target_genomes_gtdb.txt
[2023-03-18 03:45:40,530] [INFO] Task started: fastANI
[2023-03-18 03:45:40,530] [INFO] Running command: fastANI --query /var/lib/cwl/stga7ee9f73-0ddb-4fbb-9177-bd04825dfd71/OceanDNA-b35629.fa --refList OceanDNA-b35629/target_genomes_gtdb.txt --output OceanDNA-b35629/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:45:46,379] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:46,382] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:45:46,382] [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_018667355.1	s__GCA-2698665 sp018667355	77.1777	52	171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	99.95	99.92	0.96	0.95	8	-
GCA_905479195.1	s__GCA-2698665 sp905479195	76.5513	55	171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:45:46,383] [INFO] GTDB search result was written to OceanDNA-b35629/result_gtdb.tsv
[2023-03-18 03:45:46,383] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:45:46,383] [INFO] DFAST_QC result json was written to OceanDNA-b35629/dqc_result.json
[2023-03-18 03:45:46,383] [INFO] DFAST_QC completed!
[2023-03-18 03:45:46,383] [INFO] Total running time: 0h0m36s