[2023-03-16 02:38:04,914] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,914] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ad395c7-9a70-408d-8dc7-902d14ef5717/dqc_reference
[2023-03-16 02:38:06,009] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,009] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,009] [INFO] Running command: cat /var/lib/cwl/stg1807a848-7303-4209-a116-003937303759/OceanDNA-b15512.fa | prodigal -d OceanDNA-b15512/cds.fna -a OceanDNA-b15512/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:15,008] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:15,008] [INFO] Task started: HMMsearch
[2023-03-16 02:38:15,008] [INFO] Running command: hmmsearch --tblout OceanDNA-b15512/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ad395c7-9a70-408d-8dc7-902d14ef5717/dqc_reference/reference_markers.hmm OceanDNA-b15512/protein.faa > /dev/null
[2023-03-16 02:38:15,158] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:15,159] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1807a848-7303-4209-a116-003937303759/OceanDNA-b15512.fa]
[2023-03-16 02:38:15,172] [INFO] Query marker FASTA was written to OceanDNA-b15512/markers.fasta
[2023-03-16 02:38:15,173] [INFO] Task started: Blastn
[2023-03-16 02:38:15,173] [INFO] Running command: blastn -query OceanDNA-b15512/markers.fasta -db /var/lib/cwl/stg4ad395c7-9a70-408d-8dc7-902d14ef5717/dqc_reference/reference_markers.fasta -out OceanDNA-b15512/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:15,610] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:15,611] [INFO] Selected 11 target genomes.
[2023-03-16 02:38:15,611] [INFO] Target genome list was writen to OceanDNA-b15512/target_genomes.txt
[2023-03-16 02:38:15,616] [INFO] Task started: fastANI
[2023-03-16 02:38:15,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg1807a848-7303-4209-a116-003937303759/OceanDNA-b15512.fa --refList OceanDNA-b15512/target_genomes.txt --output OceanDNA-b15512/fastani_result.tsv --threads 1
[2023-03-16 02:38:22,620] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:22,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ad395c7-9a70-408d-8dc7-902d14ef5717/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:22,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ad395c7-9a70-408d-8dc7-902d14ef5717/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:22,621] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:22,621] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 02:38:22,621] [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
--------------------------------------------------------------------------------
[2023-03-16 02:38:22,621] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15512/tc_result.tsv
[2023-03-16 02:38:22,621] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:22,621] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:22,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ad395c7-9a70-408d-8dc7-902d14ef5717/dqc_reference/checkm_data
[2023-03-16 02:38:22,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:22,627] [INFO] Task started: CheckM
[2023-03-16 02:38:22,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15512/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15512/checkm_input OceanDNA-b15512/checkm_result
[2023-03-16 02:38:49,406] [INFO] Task succeeded: CheckM
[2023-03-16 02:38:49,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:38:49,408] [INFO] ===== Completeness check finished =====
[2023-03-16 02:38:49,408] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:38:49,408] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15512/markers.fasta)
[2023-03-16 02:38:49,408] [INFO] Task started: Blastn
[2023-03-16 02:38:49,408] [INFO] Running command: blastn -query OceanDNA-b15512/markers.fasta -db /var/lib/cwl/stg4ad395c7-9a70-408d-8dc7-902d14ef5717/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15512/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:49,876] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:49,877] [INFO] Selected 15 target genomes.
[2023-03-16 02:38:49,877] [INFO] Target genome list was writen to OceanDNA-b15512/target_genomes_gtdb.txt
[2023-03-16 02:38:50,246] [INFO] Task started: fastANI
[2023-03-16 02:38:50,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg1807a848-7303-4209-a116-003937303759/OceanDNA-b15512.fa --refList OceanDNA-b15512/target_genomes_gtdb.txt --output OceanDNA-b15512/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:38:56,356] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:56,362] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 02:38:56,362] [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_002401285.1	s__UBA11650 sp002401285	76.5146	81	514	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	98.75	98.75	0.80	0.80	2	-
GCA_009692925.1	s__SHYG01 sp009692925	76.395	83	514	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	99.84	99.84	0.93	0.93	2	-
GCA_002816575.1	s__UBA9611 sp002816575	76.18	62	514	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002816585.1	s__UBA9611 sp002816585	76.1572	63	514	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837355.1	s__Bin87 sp009837355	75.9675	55	514	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin87	95.0	99.97	99.97	0.97	0.97	2	-
GCA_016872385.1	s__SHYG01 sp016872385	75.9607	55	514	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840175.1	s__VXOI01 sp009840175	75.8652	69	514	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__VXOI01	95.0	99.70	99.70	0.91	0.91	2	-
GCA_002746355.1	s__UBA9611 sp002746355	75.8587	81	514	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_002238825.1	s__Bin87 sp002238825	75.7452	58	514	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin87	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:38:56,362] [INFO] GTDB search result was written to OceanDNA-b15512/result_gtdb.tsv
[2023-03-16 02:38:56,362] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:38:56,363] [INFO] DFAST_QC result json was written to OceanDNA-b15512/dqc_result.json
[2023-03-16 02:38:56,363] [INFO] DFAST_QC completed!
[2023-03-16 02:38:56,363] [INFO] Total running time: 0h0m51s