[2023-03-18 00:53:42,518] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,523] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ff324dc-5f65-4530-882d-19f98f163498/dqc_reference
[2023-03-18 00:53:43,602] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:43,603] [INFO] Task started: Prodigal
[2023-03-18 00:53:43,603] [INFO] Running command: cat /var/lib/cwl/stg8a1ea883-6413-4293-bb66-636984de9dd3/OceanDNA-b46061.fa | prodigal -d OceanDNA-b46061/cds.fna -a OceanDNA-b46061/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:54:01,644] [INFO] Task succeeded: Prodigal
[2023-03-18 00:54:01,644] [INFO] Task started: HMMsearch
[2023-03-18 00:54:01,644] [INFO] Running command: hmmsearch --tblout OceanDNA-b46061/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ff324dc-5f65-4530-882d-19f98f163498/dqc_reference/reference_markers.hmm OceanDNA-b46061/protein.faa > /dev/null
[2023-03-18 00:54:01,836] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:54:01,837] [INFO] Found 6/6 markers.
[2023-03-18 00:54:01,856] [INFO] Query marker FASTA was written to OceanDNA-b46061/markers.fasta
[2023-03-18 00:54:01,857] [INFO] Task started: Blastn
[2023-03-18 00:54:01,857] [INFO] Running command: blastn -query OceanDNA-b46061/markers.fasta -db /var/lib/cwl/stg9ff324dc-5f65-4530-882d-19f98f163498/dqc_reference/reference_markers.fasta -out OceanDNA-b46061/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:02,446] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:02,447] [INFO] Selected 15 target genomes.
[2023-03-18 00:54:02,447] [INFO] Target genome list was writen to OceanDNA-b46061/target_genomes.txt
[2023-03-18 00:54:02,458] [INFO] Task started: fastANI
[2023-03-18 00:54:02,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a1ea883-6413-4293-bb66-636984de9dd3/OceanDNA-b46061.fa --refList OceanDNA-b46061/target_genomes.txt --output OceanDNA-b46061/fastani_result.tsv --threads 1
[2023-03-18 00:54:13,274] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:13,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ff324dc-5f65-4530-882d-19f98f163498/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:13,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ff324dc-5f65-4530-882d-19f98f163498/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:13,278] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:13,278] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:13,278] [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
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	77.1302	112	692	95	below_threshold
Coraliomargarita akajimensis	strain=DSM 45221	GCA_000025905.1	395922	395922	type	True	76.4712	73	692	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:13,279] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46061/tc_result.tsv
[2023-03-18 00:54:13,279] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:13,279] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:13,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ff324dc-5f65-4530-882d-19f98f163498/dqc_reference/checkm_data
[2023-03-18 00:54:13,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:13,285] [INFO] Task started: CheckM
[2023-03-18 00:54:13,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46061/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46061/checkm_input OceanDNA-b46061/checkm_result
[2023-03-18 00:55:01,091] [INFO] Task succeeded: CheckM
[2023-03-18 00:55:01,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:55:01,117] [INFO] ===== Completeness check finished =====
[2023-03-18 00:55:01,117] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:55:01,117] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46061/markers.fasta)
[2023-03-18 00:55:01,119] [INFO] Task started: Blastn
[2023-03-18 00:55:01,119] [INFO] Running command: blastn -query OceanDNA-b46061/markers.fasta -db /var/lib/cwl/stg9ff324dc-5f65-4530-882d-19f98f163498/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46061/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:55:02,109] [INFO] Task succeeded: Blastn
[2023-03-18 00:55:02,121] [INFO] Selected 18 target genomes.
[2023-03-18 00:55:02,121] [INFO] Target genome list was writen to OceanDNA-b46061/target_genomes_gtdb.txt
[2023-03-18 00:55:02,148] [INFO] Task started: fastANI
[2023-03-18 00:55:02,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a1ea883-6413-4293-bb66-636984de9dd3/OceanDNA-b46061.fa --refList OceanDNA-b46061/target_genomes_gtdb.txt --output OceanDNA-b46061/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:55:10,605] [INFO] Task succeeded: fastANI
[2023-03-18 00:55:10,613] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:55:10,614] [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_002480015.1	s__UBA7441 sp002480015	99.459	533	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.46	97.23	0.80	0.69	7	conclusive
GCA_905182465.1	s__UBA7441 sp905182465	77.9828	147	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729725.1	s__UBA7441 sp002729725	77.9617	224	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	99.86	99.86	0.96	0.96	2	-
GCA_905479975.1	s__BACL24 sp905479975	77.626	122	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886465.1	s__UBA7441 sp009886465	77.4903	125	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	97.11	97.11	0.79	0.79	2	-
GCA_003331195.1	s__UBA7441 sp003331195	77.4266	126	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692545.1	s__UBA7441 sp007692545	77.3006	148	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854655.1	s__BACL24 sp017854655	77.2328	102	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.39	99.26	0.93	0.92	3	-
GCA_002430605.1	s__BACL24 sp002430605	77.175	116	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.69	99.69	0.90	0.90	2	-
GCA_003566795.1	s__WN38 sp003566795	77.1251	96	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292345.1	s__BACL24 sp002292345	77.0717	86	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.51	99.36	0.91	0.87	10	-
GCA_009908325.1	s__UBA7441 sp009908325	76.8995	146	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607135.1	s__BACL24 sp003485085	76.7562	85	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.81	99.81	0.84	0.84	2	-
GCF_000025905.1	s__Coraliomargarita akajimensis	76.4931	72	692	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__Coraliomargarita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:55:10,623] [INFO] GTDB search result was written to OceanDNA-b46061/result_gtdb.tsv
[2023-03-18 00:55:10,623] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:55:10,625] [INFO] DFAST_QC result json was written to OceanDNA-b46061/dqc_result.json
[2023-03-18 00:55:10,625] [INFO] DFAST_QC completed!
[2023-03-18 00:55:10,625] [INFO] Total running time: 0h1m28s