[2023-03-15 18:39:13,541] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:13,542] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:13,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg397f12a9-6e9a-4bda-ad99-5cf2267554df/dqc_reference
[2023-03-15 18:39:15,264] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:15,264] [INFO] Task started: Prodigal
[2023-03-15 18:39:15,265] [INFO] Running command: cat /var/lib/cwl/stgb586c117-6541-4b7d-a1f9-ff8b0ed74ddd/OceanDNA-b45859.fa | prodigal -d OceanDNA-b45859/cds.fna -a OceanDNA-b45859/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:56,977] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:56,978] [INFO] Task started: HMMsearch
[2023-03-15 18:39:56,978] [INFO] Running command: hmmsearch --tblout OceanDNA-b45859/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg397f12a9-6e9a-4bda-ad99-5cf2267554df/dqc_reference/reference_markers.hmm OceanDNA-b45859/protein.faa > /dev/null
[2023-03-15 18:39:57,193] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:57,193] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb586c117-6541-4b7d-a1f9-ff8b0ed74ddd/OceanDNA-b45859.fa]
[2023-03-15 18:39:57,223] [INFO] Query marker FASTA was written to OceanDNA-b45859/markers.fasta
[2023-03-15 18:39:57,224] [INFO] Task started: Blastn
[2023-03-15 18:39:57,224] [INFO] Running command: blastn -query OceanDNA-b45859/markers.fasta -db /var/lib/cwl/stg397f12a9-6e9a-4bda-ad99-5cf2267554df/dqc_reference/reference_markers.fasta -out OceanDNA-b45859/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:57,756] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:57,757] [INFO] Selected 17 target genomes.
[2023-03-15 18:39:57,757] [INFO] Target genome list was writen to OceanDNA-b45859/target_genomes.txt
[2023-03-15 18:39:57,769] [INFO] Task started: fastANI
[2023-03-15 18:39:57,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgb586c117-6541-4b7d-a1f9-ff8b0ed74ddd/OceanDNA-b45859.fa --refList OceanDNA-b45859/target_genomes.txt --output OceanDNA-b45859/fastani_result.tsv --threads 1
[2023-03-15 18:40:08,091] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:08,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg397f12a9-6e9a-4bda-ad99-5cf2267554df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:40:08,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg397f12a9-6e9a-4bda-ad99-5cf2267554df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:40:08,097] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:40:08,097] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:40:08,097] [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	77.5312	207	1485	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.0743	178	1485	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.9684	126	1485	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.4509	115	1485	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.3751	195	1485	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	74.6562	62	1485	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:40:08,098] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45859/tc_result.tsv
[2023-03-15 18:40:08,098] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:40:08,098] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:40:08,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg397f12a9-6e9a-4bda-ad99-5cf2267554df/dqc_reference/checkm_data
[2023-03-15 18:40:08,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:40:08,111] [INFO] Task started: CheckM
[2023-03-15 18:40:08,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45859/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45859/checkm_input OceanDNA-b45859/checkm_result
[2023-03-15 18:41:46,520] [INFO] Task succeeded: CheckM
[2023-03-15 18:41:46,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:41:46,523] [INFO] ===== Completeness check finished =====
[2023-03-15 18:41:46,523] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:41:46,523] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45859/markers.fasta)
[2023-03-15 18:41:46,525] [INFO] Task started: Blastn
[2023-03-15 18:41:46,525] [INFO] Running command: blastn -query OceanDNA-b45859/markers.fasta -db /var/lib/cwl/stg397f12a9-6e9a-4bda-ad99-5cf2267554df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45859/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:41:47,250] [INFO] Task succeeded: Blastn
[2023-03-15 18:41:47,251] [INFO] Selected 17 target genomes.
[2023-03-15 18:41:47,251] [INFO] Target genome list was writen to OceanDNA-b45859/target_genomes_gtdb.txt
[2023-03-15 18:41:47,923] [INFO] Task started: fastANI
[2023-03-15 18:41:47,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgb586c117-6541-4b7d-a1f9-ff8b0ed74ddd/OceanDNA-b45859.fa --refList OceanDNA-b45859/target_genomes_gtdb.txt --output OceanDNA-b45859/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:42:01,293] [INFO] Task succeeded: fastANI
[2023-03-15 18:42:01,303] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:42:01,303] [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_903859715.1	s__Opi-474 sp903859715	77.3061	152	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.98	99.96	0.98	0.96	7	-
GCA_900299415.1	s__CAIYFD01 sp900299415	77.114	86	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIYFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715765.1	s__UBA2377 sp016715765	77.0849	172	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871755.1	s__UBA6669 sp016871755	77.0473	129	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	77.0257	180	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239675.1	s__Opi-474 sp018239675	77.0116	144	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862955.1	s__Opi-474 sp903862955	76.8897	165	1485	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_018667915.1	s__M30B9 sp018667915	76.7909	82	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__M30B9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002070825.1	s__MWDT01 sp002070825	76.6721	84	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	97.04	96.87	0.67	0.67	3	-
GCA_903862595.1	s__UBA6669 sp903862595	76.6663	114	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	99.22	99.13	0.81	0.80	3	-
GCA_903948415.1	s__CAITWF01 sp903948415	76.6604	206	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879845.1	s__J108 sp014879845	76.5325	144	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__J108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402455.1	s__M30B9 sp018402455	76.4988	150	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__M30B9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650175.1	s__Ereboglobus sp001650175	76.4665	185	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848965.1	s__ER46 sp903848965	76.4063	102	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794625.1	s__UBA6669 sp016794625	76.3267	116	1485	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:42:01,303] [INFO] GTDB search result was written to OceanDNA-b45859/result_gtdb.tsv
[2023-03-15 18:42:01,303] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:42:01,305] [INFO] DFAST_QC result json was written to OceanDNA-b45859/dqc_result.json
[2023-03-15 18:42:01,305] [INFO] DFAST_QC completed!
[2023-03-15 18:42:01,305] [INFO] Total running time: 0h2m48s