[2023-03-18 20:13:32,192] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,192] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg78043c2b-5e42-4b0d-827b-321597634f86/dqc_reference
[2023-03-18 20:13:33,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,430] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,430] [INFO] Running command: cat /var/lib/cwl/stg1228ac20-343d-4f07-87ac-808ca745be4f/OceanDNA-b45857.fa | prodigal -d OceanDNA-b45857/cds.fna -a OceanDNA-b45857/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:14:21,695] [INFO] Task succeeded: Prodigal
[2023-03-18 20:14:21,695] [INFO] Task started: HMMsearch
[2023-03-18 20:14:21,695] [INFO] Running command: hmmsearch --tblout OceanDNA-b45857/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78043c2b-5e42-4b0d-827b-321597634f86/dqc_reference/reference_markers.hmm OceanDNA-b45857/protein.faa > /dev/null
[2023-03-18 20:14:21,981] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:14:21,982] [INFO] Found 6/6 markers.
[2023-03-18 20:14:22,012] [INFO] Query marker FASTA was written to OceanDNA-b45857/markers.fasta
[2023-03-18 20:14:22,013] [INFO] Task started: Blastn
[2023-03-18 20:14:22,013] [INFO] Running command: blastn -query OceanDNA-b45857/markers.fasta -db /var/lib/cwl/stg78043c2b-5e42-4b0d-827b-321597634f86/dqc_reference/reference_markers.fasta -out OceanDNA-b45857/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:26,159] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:26,160] [INFO] Selected 15 target genomes.
[2023-03-18 20:14:26,161] [INFO] Target genome list was writen to OceanDNA-b45857/target_genomes.txt
[2023-03-18 20:14:26,169] [INFO] Task started: fastANI
[2023-03-18 20:14:26,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg1228ac20-343d-4f07-87ac-808ca745be4f/OceanDNA-b45857.fa --refList OceanDNA-b45857/target_genomes.txt --output OceanDNA-b45857/fastani_result.tsv --threads 1
[2023-03-18 20:14:38,838] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:38,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78043c2b-5e42-4b0d-827b-321597634f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:38,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78043c2b-5e42-4b0d-827b-321597634f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:38,847] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:38,847] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:14:38,847] [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
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	78.3744	311	1797	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.5176	333	1797	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.4056	152	1797	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	77.3854	186	1797	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	77.2912	212	1797	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.8625	294	1797	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.0655	61	1797	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	74.9403	69	1797	95	below_threshold
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	74.7595	50	1797	95	below_threshold
Victivallis vadensis	strain=DSM 14823	GCA_003096415.1	172901	172901	type	True	74.7213	51	1797	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	74.7005	108	1797	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	74.6141	75	1797	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:14:38,847] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45857/tc_result.tsv
[2023-03-18 20:14:38,847] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:38,848] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:38,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78043c2b-5e42-4b0d-827b-321597634f86/dqc_reference/checkm_data
[2023-03-18 20:14:38,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:38,969] [INFO] Task started: CheckM
[2023-03-18 20:14:38,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45857/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45857/checkm_input OceanDNA-b45857/checkm_result
[2023-03-18 20:16:33,110] [INFO] Task succeeded: CheckM
[2023-03-18 20:16:33,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:16:33,114] [INFO] ===== Completeness check finished =====
[2023-03-18 20:16:33,114] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:16:33,114] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45857/markers.fasta)
[2023-03-18 20:16:33,115] [INFO] Task started: Blastn
[2023-03-18 20:16:33,115] [INFO] Running command: blastn -query OceanDNA-b45857/markers.fasta -db /var/lib/cwl/stg78043c2b-5e42-4b0d-827b-321597634f86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45857/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:16:33,992] [INFO] Task succeeded: Blastn
[2023-03-18 20:16:33,993] [INFO] Selected 25 target genomes.
[2023-03-18 20:16:33,993] [INFO] Target genome list was writen to OceanDNA-b45857/target_genomes_gtdb.txt
[2023-03-18 20:16:34,779] [INFO] Task started: fastANI
[2023-03-18 20:16:34,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg1228ac20-343d-4f07-87ac-808ca745be4f/OceanDNA-b45857.fa --refList OceanDNA-b45857/target_genomes_gtdb.txt --output OceanDNA-b45857/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:16:52,849] [INFO] Task succeeded: fastANI
[2023-03-18 20:16:52,861] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:16:52,861] [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_007559335.1	s__Rariglobus hedericola	78.3744	311	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876795.1	s__Rariglobus sp903876795	78.2494	310	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239845.1	s__Opitutus sp018239845	78.0243	337	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862955.1	s__Opi-474 sp903862955	77.7304	268	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.96	99.95	0.97	0.97	5	-
GCA_000242935.3	s__Geminisphaera sp000242935	77.7302	324	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	96.61	96.61	0.73	0.73	2	-
GCA_002288455.1	s__ER46 sp002288455	77.7065	320	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002070825.1	s__MWDT01 sp002070825	77.5223	148	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	97.04	96.87	0.67	0.67	3	-
GCA_016715765.1	s__UBA2377 sp016715765	77.499	295	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873805.1	s__CAIQQB01 sp903873805	77.4904	252	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIQQB01	95.0	99.97	99.97	0.95	0.95	2	-
GCA_016199925.1	s__JACQFT01 sp016199925	77.3142	257	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__JACQFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721945.1	s__Nibricoccus sp016721945	77.3081	194	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Nibricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054705.1	s__ER46 sp003054705	77.2931	307	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235555.1	s__ER46 sp016235555	77.2449	426	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650175.1	s__Ereboglobus sp001650175	77.2396	351	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794665.1	s__ER46 sp016794665	77.0894	315	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016217595.1	s__MWDT01 sp016217595	77.0758	197	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822585.1	s__Didemnitutus sp013822585	77.0331	164	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871755.1	s__UBA6669 sp016871755	77.0151	230	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903820035.1	s__ER46 sp903820035	76.9122	216	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.61	99.58	0.90	0.89	3	-
GCA_903916755.1	s__Palsa-1447 sp903916755	76.7154	161	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	99.68	99.68	0.97	0.97	2	-
GCA_016794625.1	s__UBA6669 sp016794625	76.2399	203	1797	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720725.1	s__Streptomyces rimosus_A	74.7299	127	1797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:16:52,862] [INFO] GTDB search result was written to OceanDNA-b45857/result_gtdb.tsv
[2023-03-18 20:16:52,862] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:16:52,863] [INFO] DFAST_QC result json was written to OceanDNA-b45857/dqc_result.json
[2023-03-18 20:16:52,864] [INFO] DFAST_QC completed!
[2023-03-18 20:16:52,864] [INFO] Total running time: 0h3m21s