[2023-03-18 04:04:53,881] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,881] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg72e182c6-bdbc-4f76-b31f-5df4c6a4c732/dqc_reference
[2023-03-18 04:04:55,025] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,026] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,026] [INFO] Running command: cat /var/lib/cwl/stg621ab022-4a13-4995-9c00-f3b58e00617b/OceanDNA-b42835.fa | prodigal -d OceanDNA-b42835/cds.fna -a OceanDNA-b42835/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:00,037] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:00,038] [INFO] Task started: HMMsearch
[2023-03-18 04:05:00,038] [INFO] Running command: hmmsearch --tblout OceanDNA-b42835/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72e182c6-bdbc-4f76-b31f-5df4c6a4c732/dqc_reference/reference_markers.hmm OceanDNA-b42835/protein.faa > /dev/null
[2023-03-18 04:05:00,209] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:00,209] [INFO] Found 6/6 markers.
[2023-03-18 04:05:00,219] [INFO] Query marker FASTA was written to OceanDNA-b42835/markers.fasta
[2023-03-18 04:05:00,220] [INFO] Task started: Blastn
[2023-03-18 04:05:00,220] [INFO] Running command: blastn -query OceanDNA-b42835/markers.fasta -db /var/lib/cwl/stg72e182c6-bdbc-4f76-b31f-5df4c6a4c732/dqc_reference/reference_markers.fasta -out OceanDNA-b42835/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:00,732] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:00,733] [INFO] Selected 26 target genomes.
[2023-03-18 04:05:00,733] [INFO] Target genome list was writen to OceanDNA-b42835/target_genomes.txt
[2023-03-18 04:05:00,800] [INFO] Task started: fastANI
[2023-03-18 04:05:00,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg621ab022-4a13-4995-9c00-f3b58e00617b/OceanDNA-b42835.fa --refList OceanDNA-b42835/target_genomes.txt --output OceanDNA-b42835/fastani_result.tsv --threads 1
[2023-03-18 04:05:13,451] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:13,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72e182c6-bdbc-4f76-b31f-5df4c6a4c732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:13,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72e182c6-bdbc-4f76-b31f-5df4c6a4c732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:13,455] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:05:13,455] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:05:13,455] [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
Candidatus Thioglobus autotrophicus	strain=EF1	GCA_001293165.1	1705394	1705394	type	True	76.6542	55	289	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:05:13,455] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42835/tc_result.tsv
[2023-03-18 04:05:13,455] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:13,455] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:13,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72e182c6-bdbc-4f76-b31f-5df4c6a4c732/dqc_reference/checkm_data
[2023-03-18 04:05:13,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:13,537] [INFO] Task started: CheckM
[2023-03-18 04:05:13,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42835/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42835/checkm_input OceanDNA-b42835/checkm_result
[2023-03-18 04:05:32,470] [INFO] Task succeeded: CheckM
[2023-03-18 04:05:32,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:05:32,490] [INFO] ===== Completeness check finished =====
[2023-03-18 04:05:32,490] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:05:32,491] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42835/markers.fasta)
[2023-03-18 04:05:32,492] [INFO] Task started: Blastn
[2023-03-18 04:05:32,492] [INFO] Running command: blastn -query OceanDNA-b42835/markers.fasta -db /var/lib/cwl/stg72e182c6-bdbc-4f76-b31f-5df4c6a4c732/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42835/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:33,264] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:33,270] [INFO] Selected 26 target genomes.
[2023-03-18 04:05:33,270] [INFO] Target genome list was writen to OceanDNA-b42835/target_genomes_gtdb.txt
[2023-03-18 04:05:34,144] [INFO] Task started: fastANI
[2023-03-18 04:05:34,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg621ab022-4a13-4995-9c00-f3b58e00617b/OceanDNA-b42835.fa --refList OceanDNA-b42835/target_genomes_gtdb.txt --output OceanDNA-b42835/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:05:41,869] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:41,875] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:05:41,875] [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
GCF_016592615.1	s__Ruthia sp016592615	77.2468	61	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Ruthia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845205.1	s__UBA2013 sp016845205	77.1225	89	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002909145.1	s__Thioglobus_B perditus	77.0592	51	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592595.1	s__Ruthia sp016592595	76.7928	63	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Ruthia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335045.1	s__UBA2013 sp002335045	76.7451	69	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	98.42	96.96	0.95	0.94	3	-
GCA_003489145.1	s__UBA2013 sp003489145	76.6954	54	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	99.21	98.78	0.83	0.78	42	-
GCA_015658965.1	s__UBA2013 sp015658965	76.5431	60	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648985.1	s__UBA2013 sp018648985	76.5273	53	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384345.1	s__Thioglobus pontius	76.3658	59	289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.87	99.85	0.90	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-18 04:05:41,876] [INFO] GTDB search result was written to OceanDNA-b42835/result_gtdb.tsv
[2023-03-18 04:05:41,876] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:05:41,878] [INFO] DFAST_QC result json was written to OceanDNA-b42835/dqc_result.json
[2023-03-18 04:05:41,879] [INFO] DFAST_QC completed!
[2023-03-18 04:05:41,879] [INFO] Total running time: 0h0m48s