[2023-03-19 00:33:19,043] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,043] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,043] [INFO] DQC Reference Directory: /var/lib/cwl/stga526d963-1faf-4f53-abd0-135f2d3f64b8/dqc_reference
[2023-03-19 00:33:20,215] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,216] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,216] [INFO] Running command: cat /var/lib/cwl/stg93096547-e564-4719-91d6-cd12cced9e00/OceanDNA-b12913.fa | prodigal -d OceanDNA-b12913/cds.fna -a OceanDNA-b12913/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:31,088] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:31,088] [INFO] Task started: HMMsearch
[2023-03-19 00:33:31,088] [INFO] Running command: hmmsearch --tblout OceanDNA-b12913/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga526d963-1faf-4f53-abd0-135f2d3f64b8/dqc_reference/reference_markers.hmm OceanDNA-b12913/protein.faa > /dev/null
[2023-03-19 00:33:31,280] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:31,280] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg93096547-e564-4719-91d6-cd12cced9e00/OceanDNA-b12913.fa]
[2023-03-19 00:33:31,298] [INFO] Query marker FASTA was written to OceanDNA-b12913/markers.fasta
[2023-03-19 00:33:31,304] [INFO] Task started: Blastn
[2023-03-19 00:33:31,304] [INFO] Running command: blastn -query OceanDNA-b12913/markers.fasta -db /var/lib/cwl/stga526d963-1faf-4f53-abd0-135f2d3f64b8/dqc_reference/reference_markers.fasta -out OceanDNA-b12913/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:31,817] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:31,822] [INFO] Selected 14 target genomes.
[2023-03-19 00:33:31,822] [INFO] Target genome list was writen to OceanDNA-b12913/target_genomes.txt
[2023-03-19 00:33:31,832] [INFO] Task started: fastANI
[2023-03-19 00:33:31,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg93096547-e564-4719-91d6-cd12cced9e00/OceanDNA-b12913.fa --refList OceanDNA-b12913/target_genomes.txt --output OceanDNA-b12913/fastani_result.tsv --threads 1
[2023-03-19 00:33:40,909] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:40,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga526d963-1faf-4f53-abd0-135f2d3f64b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:40,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga526d963-1faf-4f53-abd0-135f2d3f64b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:40,914] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:40,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:33:40,914] [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
Balneola vulgaris	strain=DSM 17893	GCA_000375465.1	287535	287535	type	True	77.4323	71	452	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:33:40,919] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12913/tc_result.tsv
[2023-03-19 00:33:40,919] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:40,919] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:40,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga526d963-1faf-4f53-abd0-135f2d3f64b8/dqc_reference/checkm_data
[2023-03-19 00:33:40,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:40,926] [INFO] Task started: CheckM
[2023-03-19 00:33:40,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12913/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12913/checkm_input OceanDNA-b12913/checkm_result
[2023-03-19 00:34:12,598] [INFO] Task succeeded: CheckM
[2023-03-19 00:34:12,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:34:12,602] [INFO] ===== Completeness check finished =====
[2023-03-19 00:34:12,602] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:34:12,603] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12913/markers.fasta)
[2023-03-19 00:34:12,604] [INFO] Task started: Blastn
[2023-03-19 00:34:12,604] [INFO] Running command: blastn -query OceanDNA-b12913/markers.fasta -db /var/lib/cwl/stga526d963-1faf-4f53-abd0-135f2d3f64b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12913/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:34:13,250] [INFO] Task succeeded: Blastn
[2023-03-19 00:34:13,253] [INFO] Selected 8 target genomes.
[2023-03-19 00:34:13,253] [INFO] Target genome list was writen to OceanDNA-b12913/target_genomes_gtdb.txt
[2023-03-19 00:34:13,323] [INFO] Task started: fastANI
[2023-03-19 00:34:13,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg93096547-e564-4719-91d6-cd12cced9e00/OceanDNA-b12913.fa --refList OceanDNA-b12913/target_genomes_gtdb.txt --output OceanDNA-b12913/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:34:17,565] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:17,570] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:34:17,570] [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_002364085.1	s__Balneola sp002364085	85.5877	400	452	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.57	98.41	0.97	0.85	26	-
GCA_017640785.1	s__Balneola sp017640785	81.5869	317	452	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650905.1	s__Balneola sp001650905	81.565	323	452	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	96.92	96.92	0.89	0.89	2	-
GCA_017643645.1	s__Balneola sp017643645	81.5184	332	452	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.99	99.98	1.00	0.99	5	-
GCF_000375465.1	s__Balneola vulgaris	77.4323	71	452	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640665.1	s__RHLJ01 sp017640665	77.1419	54	452	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	100.00	100.00	1.00	1.00	3	-
GCA_006969905.1	s__Balneola sp006969905	76.5896	62	452	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:34:17,572] [INFO] GTDB search result was written to OceanDNA-b12913/result_gtdb.tsv
[2023-03-19 00:34:17,573] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:34:17,576] [INFO] DFAST_QC result json was written to OceanDNA-b12913/dqc_result.json
[2023-03-19 00:34:17,576] [INFO] DFAST_QC completed!
[2023-03-19 00:34:17,576] [INFO] Total running time: 0h0m59s