[2023-03-15 08:59:47,106] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:47,106] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:47,106] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bc2441c-83f2-4bdf-8854-1178f3911aff/dqc_reference
[2023-03-15 08:59:48,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:48,192] [INFO] Task started: Prodigal
[2023-03-15 08:59:48,192] [INFO] Running command: cat /var/lib/cwl/stga875b4d9-9e77-416c-b20a-e0ee2767ab92/OceanDNA-b34221.fa | prodigal -d OceanDNA-b34221/cds.fna -a OceanDNA-b34221/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:59:57,040] [INFO] Task succeeded: Prodigal
[2023-03-15 08:59:57,040] [INFO] Task started: HMMsearch
[2023-03-15 08:59:57,040] [INFO] Running command: hmmsearch --tblout OceanDNA-b34221/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bc2441c-83f2-4bdf-8854-1178f3911aff/dqc_reference/reference_markers.hmm OceanDNA-b34221/protein.faa > /dev/null
[2023-03-15 08:59:57,210] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:59:57,211] [INFO] Found 6/6 markers.
[2023-03-15 08:59:57,220] [INFO] Query marker FASTA was written to OceanDNA-b34221/markers.fasta
[2023-03-15 08:59:57,221] [INFO] Task started: Blastn
[2023-03-15 08:59:57,221] [INFO] Running command: blastn -query OceanDNA-b34221/markers.fasta -db /var/lib/cwl/stg7bc2441c-83f2-4bdf-8854-1178f3911aff/dqc_reference/reference_markers.fasta -out OceanDNA-b34221/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:59:57,991] [INFO] Task succeeded: Blastn
[2023-03-15 08:59:57,992] [INFO] Selected 26 target genomes.
[2023-03-15 08:59:57,992] [INFO] Target genome list was writen to OceanDNA-b34221/target_genomes.txt
[2023-03-15 08:59:58,007] [INFO] Task started: fastANI
[2023-03-15 08:59:58,007] [INFO] Running command: fastANI --query /var/lib/cwl/stga875b4d9-9e77-416c-b20a-e0ee2767ab92/OceanDNA-b34221.fa --refList OceanDNA-b34221/target_genomes.txt --output OceanDNA-b34221/fastani_result.tsv --threads 1
[2023-03-15 09:00:13,342] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:13,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bc2441c-83f2-4bdf-8854-1178f3911aff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:13,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bc2441c-83f2-4bdf-8854-1178f3911aff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:13,357] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:13,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:00:13,357] [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
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.8968	118	454	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	77.7973	116	454	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	77.3653	111	454	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.3273	111	454	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.3156	112	454	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.2945	113	454	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.2565	115	454	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.226	100	454	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	77.1127	102	454	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.0914	113	454	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	77.0845	120	454	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.0768	116	454	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	77.0674	109	454	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	76.9266	105	454	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	76.8686	63	454	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	76.8467	80	454	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.8316	69	454	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	76.8277	107	454	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	76.8195	107	454	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	76.7992	113	454	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	76.7058	95	454	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	76.7035	95	454	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	76.4956	76	454	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	76.4853	77	454	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	76.4542	51	454	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.375	62	454	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:00:13,357] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34221/tc_result.tsv
[2023-03-15 09:00:13,357] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:13,357] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:13,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bc2441c-83f2-4bdf-8854-1178f3911aff/dqc_reference/checkm_data
[2023-03-15 09:00:13,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:13,361] [INFO] Task started: CheckM
[2023-03-15 09:00:13,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34221/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34221/checkm_input OceanDNA-b34221/checkm_result
[2023-03-15 09:00:39,660] [INFO] Task succeeded: CheckM
[2023-03-15 09:00:39,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:00:39,662] [INFO] ===== Completeness check finished =====
[2023-03-15 09:00:39,662] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:00:39,662] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34221/markers.fasta)
[2023-03-15 09:00:39,663] [INFO] Task started: Blastn
[2023-03-15 09:00:39,663] [INFO] Running command: blastn -query OceanDNA-b34221/markers.fasta -db /var/lib/cwl/stg7bc2441c-83f2-4bdf-8854-1178f3911aff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34221/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:41,032] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:41,032] [INFO] Selected 18 target genomes.
[2023-03-15 09:00:41,033] [INFO] Target genome list was writen to OceanDNA-b34221/target_genomes_gtdb.txt
[2023-03-15 09:00:41,053] [INFO] Task started: fastANI
[2023-03-15 09:00:41,053] [INFO] Running command: fastANI --query /var/lib/cwl/stga875b4d9-9e77-416c-b20a-e0ee2767ab92/OceanDNA-b34221.fa --refList OceanDNA-b34221/target_genomes_gtdb.txt --output OceanDNA-b34221/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:00:50,927] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:50,938] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:00:50,938] [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_009923755.1	s__UBA3065 sp009923755	99.2481	367	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3065;g__UBA3065	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018882975.1	s__UBA3065 sp018882975	83.4587	338	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3065;g__UBA3065	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009927815.1	s__UBA3065 sp002367415	81.5816	269	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3065;g__UBA3065	95.0	99.03	98.97	0.84	0.74	6	-
GCF_000310225.1	s__Thauera phenylacetica	77.7695	117	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820765.1	s__Thiobacillus sp018820765	77.4808	101	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.99	99.99	0.98	0.97	3	-
GCA_002422685.1	s__Thauera sp002422685	77.4108	115	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183655.1	s__Azospira_A sp016183655	77.3808	131	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967275.1	s__Sulfuritortus calidifontis	77.3273	111	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001922305.1	s__Thauera chlorobenzoica	77.2565	115	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.93	95.88	0.91	0.86	3	-
GCF_016653115.1	s__Rhodocyclus purpureus	77.1994	101	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469595.1	s__Thauera sp009469595	76.9703	113	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898645.1	s__SCN-69-89 sp001898645	76.8709	113	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.96	99.96	0.96	0.96	2	-
GCA_016880655.1	s__Fen-999 sp016880655	76.737	69	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002782005.1	s__Parasulfuritortus sp002782005	76.7042	50	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	99.86	99.81	0.92	0.91	9	-
GCA_015075645.1	s__VBCG01 sp015075645	76.6267	90	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	76.4927	80	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345025.1	s__Accumulibacter phosphatis_B	76.2633	68	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.42	99.42	0.93	0.93	2	-
GCA_017592775.1	s__Accumulibacter sp017592775	76.1076	89	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.29	99.29	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:00:50,938] [INFO] GTDB search result was written to OceanDNA-b34221/result_gtdb.tsv
[2023-03-15 09:00:50,938] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:00:50,941] [INFO] DFAST_QC result json was written to OceanDNA-b34221/dqc_result.json
[2023-03-15 09:00:50,941] [INFO] DFAST_QC completed!
[2023-03-15 09:00:50,941] [INFO] Total running time: 0h1m4s