[2023-03-18 01:26:26,363] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,363] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg568427bb-917f-4d61-8944-9c771c2cc7ef/dqc_reference
[2023-03-18 01:26:27,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,522] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,522] [INFO] Running command: cat /var/lib/cwl/stgc9c18681-684e-4b59-811f-d28309cc92f1/OceanDNA-b12910.fa | prodigal -d OceanDNA-b12910/cds.fna -a OceanDNA-b12910/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:48,230] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:48,231] [INFO] Task started: HMMsearch
[2023-03-18 01:26:48,231] [INFO] Running command: hmmsearch --tblout OceanDNA-b12910/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg568427bb-917f-4d61-8944-9c771c2cc7ef/dqc_reference/reference_markers.hmm OceanDNA-b12910/protein.faa > /dev/null
[2023-03-18 01:26:48,499] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:48,500] [INFO] Found 6/6 markers.
[2023-03-18 01:26:48,519] [INFO] Query marker FASTA was written to OceanDNA-b12910/markers.fasta
[2023-03-18 01:26:48,520] [INFO] Task started: Blastn
[2023-03-18 01:26:48,520] [INFO] Running command: blastn -query OceanDNA-b12910/markers.fasta -db /var/lib/cwl/stg568427bb-917f-4d61-8944-9c771c2cc7ef/dqc_reference/reference_markers.fasta -out OceanDNA-b12910/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:49,062] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:49,063] [INFO] Selected 17 target genomes.
[2023-03-18 01:26:49,063] [INFO] Target genome list was writen to OceanDNA-b12910/target_genomes.txt
[2023-03-18 01:26:49,076] [INFO] Task started: fastANI
[2023-03-18 01:26:49,076] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c18681-684e-4b59-811f-d28309cc92f1/OceanDNA-b12910.fa --refList OceanDNA-b12910/target_genomes.txt --output OceanDNA-b12910/fastani_result.tsv --threads 1
[2023-03-18 01:27:00,657] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:00,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg568427bb-917f-4d61-8944-9c771c2cc7ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:27:00,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg568427bb-917f-4d61-8944-9c771c2cc7ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:27:00,662] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:27:00,662] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:27:00,662] [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	77.5728	135	1027	95	below_threshold
Gracilimonas amylolytica	strain=LA399	GCA_002911695.1	1749045	1749045	type	True	76.6175	54	1027	95	below_threshold
Gracilimonas mengyeensis	strain=DSM 21985	GCA_900182705.1	1302730	1302730	type	True	76.4356	53	1027	95	below_threshold
Gracilimonas tropica	strain=DSM 19535	GCA_000375425.1	454600	454600	type	True	76.3546	69	1027	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:27:00,662] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12910/tc_result.tsv
[2023-03-18 01:27:00,662] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:27:00,662] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:27:00,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg568427bb-917f-4d61-8944-9c771c2cc7ef/dqc_reference/checkm_data
[2023-03-18 01:27:00,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:27:00,667] [INFO] Task started: CheckM
[2023-03-18 01:27:00,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12910/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12910/checkm_input OceanDNA-b12910/checkm_result
[2023-03-18 01:27:54,634] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:54,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:55,119] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:55,119] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:55,119] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12910/markers.fasta)
[2023-03-18 01:27:55,121] [INFO] Task started: Blastn
[2023-03-18 01:27:55,121] [INFO] Running command: blastn -query OceanDNA-b12910/markers.fasta -db /var/lib/cwl/stg568427bb-917f-4d61-8944-9c771c2cc7ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12910/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:55,944] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:55,945] [INFO] Selected 8 target genomes.
[2023-03-18 01:27:55,945] [INFO] Target genome list was writen to OceanDNA-b12910/target_genomes_gtdb.txt
[2023-03-18 01:27:55,951] [INFO] Task started: fastANI
[2023-03-18 01:27:55,951] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c18681-684e-4b59-811f-d28309cc92f1/OceanDNA-b12910.fa --refList OceanDNA-b12910/target_genomes_gtdb.txt --output OceanDNA-b12910/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:28:01,904] [INFO] Task succeeded: fastANI
[2023-03-18 01:28:01,909] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:28:01,909] [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_017643645.1	s__Balneola sp017643645	89.4318	853	1027	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.99	99.98	1.00	0.99	5	-
GCF_001650905.1	s__Balneola sp001650905	89.3241	817	1027	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	96.92	96.92	0.89	0.89	2	-
GCA_017640785.1	s__Balneola sp017640785	89.0038	808	1027	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364085.1	s__Balneola sp002364085	85.5627	729	1027	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.57	98.41	0.97	0.85	26	-
GCF_000375465.1	s__Balneola vulgaris	77.5728	135	1027	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694685.1	s__Gracilimonas sp002694685	76.6	84	1027	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	-
GCA_006969905.1	s__Balneola sp006969905	76.2135	106	1027	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:28:01,909] [INFO] GTDB search result was written to OceanDNA-b12910/result_gtdb.tsv
[2023-03-18 01:28:01,910] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:28:01,910] [INFO] DFAST_QC result json was written to OceanDNA-b12910/dqc_result.json
[2023-03-18 01:28:01,911] [INFO] DFAST_QC completed!
[2023-03-18 01:28:01,911] [INFO] Total running time: 0h1m36s