[2023-03-18 02:13:13,420] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:13:13,420] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:13:13,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg68f8f4db-b032-416c-85d2-06327bd9b2ea/dqc_reference
[2023-03-18 02:13:14,504] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:13:14,505] [INFO] Task started: Prodigal
[2023-03-18 02:13:14,505] [INFO] Running command: cat /var/lib/cwl/stg496b48fa-28a0-425d-8962-49f87a678d06/OceanDNA-b45853.fa | prodigal -d OceanDNA-b45853/cds.fna -a OceanDNA-b45853/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:13:46,126] [INFO] Task succeeded: Prodigal
[2023-03-18 02:13:46,127] [INFO] Task started: HMMsearch
[2023-03-18 02:13:46,127] [INFO] Running command: hmmsearch --tblout OceanDNA-b45853/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68f8f4db-b032-416c-85d2-06327bd9b2ea/dqc_reference/reference_markers.hmm OceanDNA-b45853/protein.faa > /dev/null
[2023-03-18 02:13:46,322] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:13:46,323] [INFO] Found 6/6 markers.
[2023-03-18 02:13:46,348] [INFO] Query marker FASTA was written to OceanDNA-b45853/markers.fasta
[2023-03-18 02:13:46,349] [INFO] Task started: Blastn
[2023-03-18 02:13:46,349] [INFO] Running command: blastn -query OceanDNA-b45853/markers.fasta -db /var/lib/cwl/stg68f8f4db-b032-416c-85d2-06327bd9b2ea/dqc_reference/reference_markers.fasta -out OceanDNA-b45853/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:13:46,968] [INFO] Task succeeded: Blastn
[2023-03-18 02:13:46,996] [INFO] Selected 15 target genomes.
[2023-03-18 02:13:46,996] [INFO] Target genome list was writen to OceanDNA-b45853/target_genomes.txt
[2023-03-18 02:13:47,006] [INFO] Task started: fastANI
[2023-03-18 02:13:47,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg496b48fa-28a0-425d-8962-49f87a678d06/OceanDNA-b45853.fa --refList OceanDNA-b45853/target_genomes.txt --output OceanDNA-b45853/fastani_result.tsv --threads 1
[2023-03-18 02:13:57,381] [INFO] Task succeeded: fastANI
[2023-03-18 02:13:57,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68f8f4db-b032-416c-85d2-06327bd9b2ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:13:57,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68f8f4db-b032-416c-85d2-06327bd9b2ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:13:57,386] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:13:57,386] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:13:57,386] [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	76.7443	83	1171	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.6056	64	1171	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.174	55	1171	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	75.8329	56	1171	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:13:57,386] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45853/tc_result.tsv
[2023-03-18 02:13:57,386] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:13:57,386] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:13:57,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68f8f4db-b032-416c-85d2-06327bd9b2ea/dqc_reference/checkm_data
[2023-03-18 02:13:57,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:13:57,393] [INFO] Task started: CheckM
[2023-03-18 02:13:57,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45853/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45853/checkm_input OceanDNA-b45853/checkm_result
[2023-03-18 02:15:15,263] [INFO] Task succeeded: CheckM
[2023-03-18 02:15:15,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:15:15,302] [INFO] ===== Completeness check finished =====
[2023-03-18 02:15:15,303] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:15:15,303] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45853/markers.fasta)
[2023-03-18 02:15:15,305] [INFO] Task started: Blastn
[2023-03-18 02:15:15,305] [INFO] Running command: blastn -query OceanDNA-b45853/markers.fasta -db /var/lib/cwl/stg68f8f4db-b032-416c-85d2-06327bd9b2ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45853/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:15:16,335] [INFO] Task succeeded: Blastn
[2023-03-18 02:15:16,336] [INFO] Selected 19 target genomes.
[2023-03-18 02:15:16,336] [INFO] Target genome list was writen to OceanDNA-b45853/target_genomes_gtdb.txt
[2023-03-18 02:15:16,380] [INFO] Task started: fastANI
[2023-03-18 02:15:16,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg496b48fa-28a0-425d-8962-49f87a678d06/OceanDNA-b45853.fa --refList OceanDNA-b45853/target_genomes_gtdb.txt --output OceanDNA-b45853/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:15:28,935] [INFO] Task succeeded: fastANI
[2023-03-18 02:15:28,944] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:15:28,944] [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_018667915.1	s__M30B9 sp018667915	99.8707	1077	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__M30B9	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018402455.1	s__M30B9 sp018402455	77.5169	214	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__M30B9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559335.1	s__Rariglobus hedericola	76.7443	83	1171	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	76.6445	68	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187945.1	s__Didemnitutus sp016187945	76.5529	61	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746835.1	s__Lacunisphaera limnophila	76.4866	58	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830425.1	s__Opi-474 sp903830425	76.3984	57	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_903862595.1	s__UBA6669 sp903862595	76.3424	51	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	99.22	99.13	0.81	0.80	3	-
GCF_003054705.1	s__ER46 sp003054705	76.2871	55	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871755.1	s__UBA6669 sp016871755	76.2105	62	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000171235.2	s__Geminisphaera colitermitum	76.174	55	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	97.34	97.31	0.79	0.79	3	-
GCA_903881475.1	s__Opi-474 sp903881475	76.1613	52	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.50	98.31	0.92	0.83	9	-
GCA_016715765.1	s__UBA2377 sp016715765	76.1455	55	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239675.1	s__Opi-474 sp018239675	75.9345	53	1171	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:15:28,944] [INFO] GTDB search result was written to OceanDNA-b45853/result_gtdb.tsv
[2023-03-18 02:15:28,944] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:15:28,945] [INFO] DFAST_QC result json was written to OceanDNA-b45853/dqc_result.json
[2023-03-18 02:15:28,945] [INFO] DFAST_QC completed!
[2023-03-18 02:15:28,945] [INFO] Total running time: 0h2m16s