[2023-03-14 12:56:20,971] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:56:20,971] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:56:20,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgb556abcc-90fa-4bec-8aa4-1e3abfb24ea9/dqc_reference
[2023-03-14 12:56:22,062] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:56:22,063] [INFO] Task started: Prodigal
[2023-03-14 12:56:22,063] [INFO] Running command: cat /var/lib/cwl/stgfd5935d2-7f16-469e-8ea5-a4da1f80edb0/OceanDNA-b12980.fa | prodigal -d OceanDNA-b12980/cds.fna -a OceanDNA-b12980/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:56:50,067] [INFO] Task succeeded: Prodigal
[2023-03-14 12:56:50,067] [INFO] Task started: HMMsearch
[2023-03-14 12:56:50,067] [INFO] Running command: hmmsearch --tblout OceanDNA-b12980/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb556abcc-90fa-4bec-8aa4-1e3abfb24ea9/dqc_reference/reference_markers.hmm OceanDNA-b12980/protein.faa > /dev/null
[2023-03-14 12:56:50,267] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:56:50,267] [INFO] Found 6/6 markers.
[2023-03-14 12:56:50,290] [INFO] Query marker FASTA was written to OceanDNA-b12980/markers.fasta
[2023-03-14 12:56:50,291] [INFO] Task started: Blastn
[2023-03-14 12:56:50,291] [INFO] Running command: blastn -query OceanDNA-b12980/markers.fasta -db /var/lib/cwl/stgb556abcc-90fa-4bec-8aa4-1e3abfb24ea9/dqc_reference/reference_markers.fasta -out OceanDNA-b12980/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:56:50,821] [INFO] Task succeeded: Blastn
[2023-03-14 12:56:50,821] [INFO] Selected 18 target genomes.
[2023-03-14 12:56:50,822] [INFO] Target genome list was writen to OceanDNA-b12980/target_genomes.txt
[2023-03-14 12:56:50,833] [INFO] Task started: fastANI
[2023-03-14 12:56:50,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd5935d2-7f16-469e-8ea5-a4da1f80edb0/OceanDNA-b12980.fa --refList OceanDNA-b12980/target_genomes.txt --output OceanDNA-b12980/fastani_result.tsv --threads 1
[2023-03-14 12:57:11,907] [INFO] Task succeeded: fastANI
[2023-03-14 12:57:11,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb556abcc-90fa-4bec-8aa4-1e3abfb24ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:57:11,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb556abcc-90fa-4bec-8aa4-1e3abfb24ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:57:11,912] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:57:11,912] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:57:11,912] [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
Gracilimonas tropica	strain=DSM 19535	GCA_000375425.1	454600	454600	type	True	79.243	537	1249	95	below_threshold
Gracilimonas amylolytica	strain=LA399	GCA_002911695.1	1749045	1749045	type	True	77.8785	313	1249	95	below_threshold
Gracilimonas mengyeensis	strain=DSM 21985	GCA_900182705.1	1302730	1302730	type	True	77.4835	278	1249	95	below_threshold
Balneola vulgaris	strain=DSM 17893	GCA_000375465.1	287535	287535	type	True	76.0426	50	1249	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:57:11,913] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12980/tc_result.tsv
[2023-03-14 12:57:11,913] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:57:11,913] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:57:11,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb556abcc-90fa-4bec-8aa4-1e3abfb24ea9/dqc_reference/checkm_data
[2023-03-14 12:57:11,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:57:11,920] [INFO] Task started: CheckM
[2023-03-14 12:57:11,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12980/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12980/checkm_input OceanDNA-b12980/checkm_result
[2023-03-14 12:58:38,766] [INFO] Task succeeded: CheckM
[2023-03-14 12:58:38,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:58:38,770] [INFO] ===== Completeness check finished =====
[2023-03-14 12:58:38,770] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:58:38,770] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12980/markers.fasta)
[2023-03-14 12:58:38,771] [INFO] Task started: Blastn
[2023-03-14 12:58:38,771] [INFO] Running command: blastn -query OceanDNA-b12980/markers.fasta -db /var/lib/cwl/stgb556abcc-90fa-4bec-8aa4-1e3abfb24ea9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12980/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:58:39,510] [INFO] Task succeeded: Blastn
[2023-03-14 12:58:39,511] [INFO] Selected 14 target genomes.
[2023-03-14 12:58:39,511] [INFO] Target genome list was writen to OceanDNA-b12980/target_genomes_gtdb.txt
[2023-03-14 12:58:39,530] [INFO] Task started: fastANI
[2023-03-14 12:58:39,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd5935d2-7f16-469e-8ea5-a4da1f80edb0/OceanDNA-b12980.fa --refList OceanDNA-b12980/target_genomes_gtdb.txt --output OceanDNA-b12980/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:58:50,488] [INFO] Task succeeded: fastANI
[2023-03-14 12:58:50,494] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:58:50,494] [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_002696035.1	s__Gracilimonas sp002696035	99.9976	1236	1249	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000375425.1	s__Gracilimonas tropica	79.246	536	1249	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762685.1	s__Gracilimonas sp014762685	78.3167	270	1249	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002911695.1	s__Gracilimonas amylolytica	77.9005	311	1249	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694685.1	s__Gracilimonas sp002694685	77.8985	265	1249	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	-
GCA_017641085.1	s__Gracilimonas sp017641085	77.8543	341	1249	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900182705.1	s__Gracilimonas mengyeensis	77.4835	278	1249	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711805.1	s__MES10 sp009711805	76.7572	114	1249	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__MES10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:58:50,495] [INFO] GTDB search result was written to OceanDNA-b12980/result_gtdb.tsv
[2023-03-14 12:58:50,495] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:58:50,496] [INFO] DFAST_QC result json was written to OceanDNA-b12980/dqc_result.json
[2023-03-14 12:58:50,497] [INFO] DFAST_QC completed!
[2023-03-14 12:58:50,497] [INFO] Total running time: 0h2m30s