[2023-03-15 13:20:51,578] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,579] [INFO] DQC Reference Directory: /var/lib/cwl/stgb82ab14a-2e00-47df-bff8-70475818087c/dqc_reference
[2023-03-15 13:20:52,666] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,666] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,666] [INFO] Running command: cat /var/lib/cwl/stg5b2e63f6-df46-4745-8c75-1cf9f2b09e76/OceanDNA-b12943.fa | prodigal -d OceanDNA-b12943/cds.fna -a OceanDNA-b12943/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:13,852] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:13,852] [INFO] Task started: HMMsearch
[2023-03-15 13:21:13,852] [INFO] Running command: hmmsearch --tblout OceanDNA-b12943/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb82ab14a-2e00-47df-bff8-70475818087c/dqc_reference/reference_markers.hmm OceanDNA-b12943/protein.faa > /dev/null
[2023-03-15 13:21:14,120] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:14,120] [INFO] Found 6/6 markers.
[2023-03-15 13:21:14,141] [INFO] Query marker FASTA was written to OceanDNA-b12943/markers.fasta
[2023-03-15 13:21:14,141] [INFO] Task started: Blastn
[2023-03-15 13:21:14,141] [INFO] Running command: blastn -query OceanDNA-b12943/markers.fasta -db /var/lib/cwl/stgb82ab14a-2e00-47df-bff8-70475818087c/dqc_reference/reference_markers.fasta -out OceanDNA-b12943/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:14,696] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:14,698] [INFO] Selected 20 target genomes.
[2023-03-15 13:21:14,698] [INFO] Target genome list was writen to OceanDNA-b12943/target_genomes.txt
[2023-03-15 13:21:14,716] [INFO] Task started: fastANI
[2023-03-15 13:21:14,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2e63f6-df46-4745-8c75-1cf9f2b09e76/OceanDNA-b12943.fa --refList OceanDNA-b12943/target_genomes.txt --output OceanDNA-b12943/fastani_result.tsv --threads 1
[2023-03-15 13:21:27,191] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:27,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb82ab14a-2e00-47df-bff8-70475818087c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:27,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb82ab14a-2e00-47df-bff8-70475818087c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:27,197] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:27,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:27,197] [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	77.6529	139	1061	95	below_threshold
Gracilimonas tropica	strain=DSM 19535	GCA_000375425.1	454600	454600	type	True	76.0108	73	1061	95	below_threshold
Gracilimonas amylolytica	strain=LA399	GCA_002911695.1	1749045	1749045	type	True	75.9522	67	1061	95	below_threshold
Gracilimonas mengyeensis	strain=DSM 21985	GCA_900182705.1	1302730	1302730	type	True	75.9269	57	1061	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:27,197] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12943/tc_result.tsv
[2023-03-15 13:21:27,197] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:27,197] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:27,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb82ab14a-2e00-47df-bff8-70475818087c/dqc_reference/checkm_data
[2023-03-15 13:21:27,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:27,204] [INFO] Task started: CheckM
[2023-03-15 13:21:27,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12943/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12943/checkm_input OceanDNA-b12943/checkm_result
[2023-03-15 13:22:22,172] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:22,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:22,175] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:22,175] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:22,176] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12943/markers.fasta)
[2023-03-15 13:22:22,176] [INFO] Task started: Blastn
[2023-03-15 13:22:22,177] [INFO] Running command: blastn -query OceanDNA-b12943/markers.fasta -db /var/lib/cwl/stgb82ab14a-2e00-47df-bff8-70475818087c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12943/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:22,931] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:22,933] [INFO] Selected 9 target genomes.
[2023-03-15 13:22:22,933] [INFO] Target genome list was writen to OceanDNA-b12943/target_genomes_gtdb.txt
[2023-03-15 13:22:22,962] [INFO] Task started: fastANI
[2023-03-15 13:22:22,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2e63f6-df46-4745-8c75-1cf9f2b09e76/OceanDNA-b12943.fa --refList OceanDNA-b12943/target_genomes_gtdb.txt --output OceanDNA-b12943/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:29,087] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:29,093] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:22:29,093] [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	99.9629	1040	1061	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.57	98.41	0.97	0.85	26	conclusive
GCA_017640785.1	s__Balneola sp017640785	86.2219	771	1061	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643645.1	s__Balneola sp017643645	86.0234	778	1061	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	85.6958	741	1061	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	96.92	96.92	0.89	0.89	2	-
GCF_000375465.1	s__Balneola vulgaris	77.6529	139	1061	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	76.2623	88	1061	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	-
GCA_003712055.1	s__RHLJ01 sp003712055	76.1664	88	1061	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375425.1	s__Gracilimonas tropica	76.0108	73	1061	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:29,094] [INFO] GTDB search result was written to OceanDNA-b12943/result_gtdb.tsv
[2023-03-15 13:22:29,094] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:29,096] [INFO] DFAST_QC result json was written to OceanDNA-b12943/dqc_result.json
[2023-03-15 13:22:29,096] [INFO] DFAST_QC completed!
[2023-03-15 13:22:29,096] [INFO] Total running time: 0h1m38s