[2023-03-18 02:20:58,599] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:20:58,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:20:58,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg983ff3b2-ee76-4096-b319-0ed0a3be7b4d/dqc_reference
[2023-03-18 02:20:59,735] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:20:59,735] [INFO] Task started: Prodigal
[2023-03-18 02:20:59,735] [INFO] Running command: cat /var/lib/cwl/stgd26a072e-028a-4106-94dd-f50b5566a26d/OceanDNA-b32516.fa | prodigal -d OceanDNA-b32516/cds.fna -a OceanDNA-b32516/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:21:04,052] [INFO] Task succeeded: Prodigal
[2023-03-18 02:21:04,053] [INFO] Task started: HMMsearch
[2023-03-18 02:21:04,053] [INFO] Running command: hmmsearch --tblout OceanDNA-b32516/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg983ff3b2-ee76-4096-b319-0ed0a3be7b4d/dqc_reference/reference_markers.hmm OceanDNA-b32516/protein.faa > /dev/null
[2023-03-18 02:21:04,196] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:21:04,196] [INFO] Found 6/6 markers.
[2023-03-18 02:21:04,205] [INFO] Query marker FASTA was written to OceanDNA-b32516/markers.fasta
[2023-03-18 02:21:04,207] [INFO] Task started: Blastn
[2023-03-18 02:21:04,207] [INFO] Running command: blastn -query OceanDNA-b32516/markers.fasta -db /var/lib/cwl/stg983ff3b2-ee76-4096-b319-0ed0a3be7b4d/dqc_reference/reference_markers.fasta -out OceanDNA-b32516/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:21:04,757] [INFO] Task succeeded: Blastn
[2023-03-18 02:21:04,757] [INFO] Selected 11 target genomes.
[2023-03-18 02:21:04,758] [INFO] Target genome list was writen to OceanDNA-b32516/target_genomes.txt
[2023-03-18 02:21:04,763] [INFO] Task started: fastANI
[2023-03-18 02:21:04,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgd26a072e-028a-4106-94dd-f50b5566a26d/OceanDNA-b32516.fa --refList OceanDNA-b32516/target_genomes.txt --output OceanDNA-b32516/fastani_result.tsv --threads 1
[2023-03-18 02:21:08,409] [INFO] Task succeeded: fastANI
[2023-03-18 02:21:08,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg983ff3b2-ee76-4096-b319-0ed0a3be7b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:21:08,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg983ff3b2-ee76-4096-b319-0ed0a3be7b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:21:08,410] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:21:08,410] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:21:08,410] [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 02:21:08,410] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32516/tc_result.tsv
[2023-03-18 02:21:08,410] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:21:08,410] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:21:08,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg983ff3b2-ee76-4096-b319-0ed0a3be7b4d/dqc_reference/checkm_data
[2023-03-18 02:21:08,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:21:08,415] [INFO] Task started: CheckM
[2023-03-18 02:21:08,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32516/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32516/checkm_input OceanDNA-b32516/checkm_result
[2023-03-18 02:21:25,476] [INFO] Task succeeded: CheckM
[2023-03-18 02:21:25,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.95%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:21:25,478] [INFO] ===== Completeness check finished =====
[2023-03-18 02:21:25,478] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:21:25,478] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32516/markers.fasta)
[2023-03-18 02:21:25,480] [INFO] Task started: Blastn
[2023-03-18 02:21:25,480] [INFO] Running command: blastn -query OceanDNA-b32516/markers.fasta -db /var/lib/cwl/stg983ff3b2-ee76-4096-b319-0ed0a3be7b4d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32516/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:21:26,188] [INFO] Task succeeded: Blastn
[2023-03-18 02:21:26,189] [INFO] Selected 23 target genomes.
[2023-03-18 02:21:26,189] [INFO] Target genome list was writen to OceanDNA-b32516/target_genomes_gtdb.txt
[2023-03-18 02:21:26,243] [INFO] Task started: fastANI
[2023-03-18 02:21:26,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgd26a072e-028a-4106-94dd-f50b5566a26d/OceanDNA-b32516.fa --refList OceanDNA-b32516/target_genomes_gtdb.txt --output OceanDNA-b32516/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:21:30,684] [INFO] Task succeeded: fastANI
[2023-03-18 02:21:30,687] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:21:30,687] [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_002711515.1	s__GCA-2711515 sp002711515	98.4972	147	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2711515	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902563505.1	s__GCA-2711515 sp902563505	76.6719	56	203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2711515	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:21:30,687] [INFO] GTDB search result was written to OceanDNA-b32516/result_gtdb.tsv
[2023-03-18 02:21:30,687] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:21:30,688] [INFO] DFAST_QC result json was written to OceanDNA-b32516/dqc_result.json
[2023-03-18 02:21:30,688] [INFO] DFAST_QC completed!
[2023-03-18 02:21:30,688] [INFO] Total running time: 0h0m32s