[2023-03-17 05:34:58,168] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:34:58,168] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:34:58,168] [INFO] DQC Reference Directory: /var/lib/cwl/stge1cd5ce7-cdb5-411c-b548-99910fe32cb1/dqc_reference
[2023-03-17 05:34:59,279] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:34:59,279] [INFO] Task started: Prodigal
[2023-03-17 05:34:59,280] [INFO] Running command: cat /var/lib/cwl/stgf36c69b0-febf-4ed8-aab3-dffb56bad468/OceanDNA-b33920.fa | prodigal -d OceanDNA-b33920/cds.fna -a OceanDNA-b33920/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:35:04,440] [INFO] Task succeeded: Prodigal
[2023-03-17 05:35:04,441] [INFO] Task started: HMMsearch
[2023-03-17 05:35:04,441] [INFO] Running command: hmmsearch --tblout OceanDNA-b33920/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1cd5ce7-cdb5-411c-b548-99910fe32cb1/dqc_reference/reference_markers.hmm OceanDNA-b33920/protein.faa > /dev/null
[2023-03-17 05:35:04,599] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:35:04,599] [INFO] Found 6/6 markers.
[2023-03-17 05:35:04,616] [INFO] Query marker FASTA was written to OceanDNA-b33920/markers.fasta
[2023-03-17 05:35:04,617] [INFO] Task started: Blastn
[2023-03-17 05:35:04,617] [INFO] Running command: blastn -query OceanDNA-b33920/markers.fasta -db /var/lib/cwl/stge1cd5ce7-cdb5-411c-b548-99910fe32cb1/dqc_reference/reference_markers.fasta -out OceanDNA-b33920/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:05,120] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:05,121] [INFO] Selected 24 target genomes.
[2023-03-17 05:35:05,121] [INFO] Target genome list was writen to OceanDNA-b33920/target_genomes.txt
[2023-03-17 05:35:05,133] [INFO] Task started: fastANI
[2023-03-17 05:35:05,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgf36c69b0-febf-4ed8-aab3-dffb56bad468/OceanDNA-b33920.fa --refList OceanDNA-b33920/target_genomes.txt --output OceanDNA-b33920/fastani_result.tsv --threads 1
[2023-03-17 05:35:13,504] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:13,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1cd5ce7-cdb5-411c-b548-99910fe32cb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:35:13,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1cd5ce7-cdb5-411c-b548-99910fe32cb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:35:13,505] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:35:13,505] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:35:13,505] [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 05:35:13,506] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33920/tc_result.tsv
[2023-03-17 05:35:13,507] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:35:13,508] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:35:13,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1cd5ce7-cdb5-411c-b548-99910fe32cb1/dqc_reference/checkm_data
[2023-03-17 05:35:13,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:35:13,550] [INFO] Task started: CheckM
[2023-03-17 05:35:13,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33920/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33920/checkm_input OceanDNA-b33920/checkm_result
[2023-03-17 05:35:32,273] [INFO] Task succeeded: CheckM
[2023-03-17 05:35:32,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:35:32,300] [INFO] ===== Completeness check finished =====
[2023-03-17 05:35:32,300] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:35:32,300] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33920/markers.fasta)
[2023-03-17 05:35:32,302] [INFO] Task started: Blastn
[2023-03-17 05:35:32,302] [INFO] Running command: blastn -query OceanDNA-b33920/markers.fasta -db /var/lib/cwl/stge1cd5ce7-cdb5-411c-b548-99910fe32cb1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33920/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:33,018] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:33,020] [INFO] Selected 24 target genomes.
[2023-03-17 05:35:33,020] [INFO] Target genome list was writen to OceanDNA-b33920/target_genomes_gtdb.txt
[2023-03-17 05:35:33,198] [INFO] Task started: fastANI
[2023-03-17 05:35:33,199] [INFO] Running command: fastANI --query /var/lib/cwl/stgf36c69b0-febf-4ed8-aab3-dffb56bad468/OceanDNA-b33920.fa --refList OceanDNA-b33920/target_genomes_gtdb.txt --output OceanDNA-b33920/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:35:39,149] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:39,151] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:35:39,151] [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_905182075.1	s__BACL14 sp905182075	85.4413	256	341	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618945.1	s__BACL14 sp905618945	77.7247	70	341	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 05:35:39,156] [INFO] GTDB search result was written to OceanDNA-b33920/result_gtdb.tsv
[2023-03-17 05:35:39,163] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:35:39,168] [INFO] DFAST_QC result json was written to OceanDNA-b33920/dqc_result.json
[2023-03-17 05:35:39,168] [INFO] DFAST_QC completed!
[2023-03-17 05:35:39,168] [INFO] Total running time: 0h0m41s