[2023-03-19 04:11:06,922] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg53b8c105-d49b-406f-a921-fa63debe016f/dqc_reference
[2023-03-19 04:11:08,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,544] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,544] [INFO] Running command: cat /var/lib/cwl/stg4c517aa1-787d-4488-871c-8ac924971f09/OceanDNA-b22160.fa | prodigal -d OceanDNA-b22160/cds.fna -a OceanDNA-b22160/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:15,335] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:15,336] [INFO] Task started: HMMsearch
[2023-03-19 04:11:15,336] [INFO] Running command: hmmsearch --tblout OceanDNA-b22160/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53b8c105-d49b-406f-a921-fa63debe016f/dqc_reference/reference_markers.hmm OceanDNA-b22160/protein.faa > /dev/null
[2023-03-19 04:11:15,550] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:15,550] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4c517aa1-787d-4488-871c-8ac924971f09/OceanDNA-b22160.fa]
[2023-03-19 04:11:15,562] [INFO] Query marker FASTA was written to OceanDNA-b22160/markers.fasta
[2023-03-19 04:11:15,564] [INFO] Task started: Blastn
[2023-03-19 04:11:15,564] [INFO] Running command: blastn -query OceanDNA-b22160/markers.fasta -db /var/lib/cwl/stg53b8c105-d49b-406f-a921-fa63debe016f/dqc_reference/reference_markers.fasta -out OceanDNA-b22160/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:18,727] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:18,727] [INFO] Selected 15 target genomes.
[2023-03-19 04:11:18,728] [INFO] Target genome list was writen to OceanDNA-b22160/target_genomes.txt
[2023-03-19 04:11:18,737] [INFO] Task started: fastANI
[2023-03-19 04:11:18,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c517aa1-787d-4488-871c-8ac924971f09/OceanDNA-b22160.fa --refList OceanDNA-b22160/target_genomes.txt --output OceanDNA-b22160/fastani_result.tsv --threads 1
[2023-03-19 04:11:27,358] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:27,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53b8c105-d49b-406f-a921-fa63debe016f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:27,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53b8c105-d49b-406f-a921-fa63debe016f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:27,359] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:27,359] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:11:27,359] [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
--------------------------------------------------------------------------------
[2023-03-19 04:11:27,359] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22160/tc_result.tsv
[2023-03-19 04:11:27,359] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:27,359] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:27,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53b8c105-d49b-406f-a921-fa63debe016f/dqc_reference/checkm_data
[2023-03-19 04:11:27,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:27,365] [INFO] Task started: CheckM
[2023-03-19 04:11:27,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22160/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22160/checkm_input OceanDNA-b22160/checkm_result
[2023-03-19 04:11:52,227] [INFO] Task succeeded: CheckM
[2023-03-19 04:11:52,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:11:52,229] [INFO] ===== Completeness check finished =====
[2023-03-19 04:11:52,230] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:11:52,230] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22160/markers.fasta)
[2023-03-19 04:11:52,232] [INFO] Task started: Blastn
[2023-03-19 04:11:52,232] [INFO] Running command: blastn -query OceanDNA-b22160/markers.fasta -db /var/lib/cwl/stg53b8c105-d49b-406f-a921-fa63debe016f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22160/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:53,065] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:53,066] [INFO] Selected 11 target genomes.
[2023-03-19 04:11:53,066] [INFO] Target genome list was writen to OceanDNA-b22160/target_genomes_gtdb.txt
[2023-03-19 04:11:53,170] [INFO] Task started: fastANI
[2023-03-19 04:11:53,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c517aa1-787d-4488-871c-8ac924971f09/OceanDNA-b22160.fa --refList OceanDNA-b22160/target_genomes_gtdb.txt --output OceanDNA-b22160/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:11:56,557] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:56,562] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:11:56,562] [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_018701395.1	s__GCA-002718515 sp018701395	99.5658	329	346	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.63	99.41	0.94	0.92	4	conclusive
GCA_012965315.1	s__GCA-002718515 sp012965315	92.2945	298	346	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.71	99.67	0.87	0.85	4	-
GCA_014238785.1	s__GCA-002718515 sp014238785	79.2472	111	346	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689385.1	s__GCA-002718515 sp002689385	78.2243	110	346	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018657585.1	s__GCA-002718515 sp018657585	77.9398	61	346	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381385.1	s__GCA-002718515 sp014381385	77.0957	69	346	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:11:56,562] [INFO] GTDB search result was written to OceanDNA-b22160/result_gtdb.tsv
[2023-03-19 04:11:56,562] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:11:56,563] [INFO] DFAST_QC result json was written to OceanDNA-b22160/dqc_result.json
[2023-03-19 04:11:56,563] [INFO] DFAST_QC completed!
[2023-03-19 04:11:56,563] [INFO] Total running time: 0h0m50s