[2023-03-15 13:20:51,597] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,597] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg7876ee2b-e88b-4c7e-8c84-245f93a3c3af/dqc_reference
[2023-03-15 13:20:52,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,701] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,701] [INFO] Running command: cat /var/lib/cwl/stge0cd44be-e7b8-477c-bc12-42c2a782c3a5/OceanDNA-b34126.fa | prodigal -d OceanDNA-b34126/cds.fna -a OceanDNA-b34126/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:16,302] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:16,303] [INFO] Task started: HMMsearch
[2023-03-15 13:21:16,303] [INFO] Running command: hmmsearch --tblout OceanDNA-b34126/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7876ee2b-e88b-4c7e-8c84-245f93a3c3af/dqc_reference/reference_markers.hmm OceanDNA-b34126/protein.faa > /dev/null
[2023-03-15 13:21:16,581] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:16,582] [INFO] Found 6/6 markers.
[2023-03-15 13:21:16,606] [INFO] Query marker FASTA was written to OceanDNA-b34126/markers.fasta
[2023-03-15 13:21:16,608] [INFO] Task started: Blastn
[2023-03-15 13:21:16,608] [INFO] Running command: blastn -query OceanDNA-b34126/markers.fasta -db /var/lib/cwl/stg7876ee2b-e88b-4c7e-8c84-245f93a3c3af/dqc_reference/reference_markers.fasta -out OceanDNA-b34126/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:17,418] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:17,419] [INFO] Selected 26 target genomes.
[2023-03-15 13:21:17,419] [INFO] Target genome list was writen to OceanDNA-b34126/target_genomes.txt
[2023-03-15 13:21:17,437] [INFO] Task started: fastANI
[2023-03-15 13:21:17,438] [INFO] Running command: fastANI --query /var/lib/cwl/stge0cd44be-e7b8-477c-bc12-42c2a782c3a5/OceanDNA-b34126.fa --refList OceanDNA-b34126/target_genomes.txt --output OceanDNA-b34126/fastani_result.tsv --threads 1
[2023-03-15 13:21:36,924] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:36,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7876ee2b-e88b-4c7e-8c84-245f93a3c3af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:36,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7876ee2b-e88b-4c7e-8c84-245f93a3c3af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:36,943] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:36,943] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:36,943] [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 phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.9577	392	1213	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.8209	421	1213	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	78.8148	383	1213	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	78.7853	426	1213	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	78.7769	376	1213	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.7525	402	1213	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.7066	406	1213	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	78.7	447	1213	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	78.6785	421	1213	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.6685	399	1213	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	78.6042	414	1213	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	78.5972	414	1213	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	78.5799	404	1213	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	78.5643	401	1213	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.5423	391	1213	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	78.5303	393	1213	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	78.4045	387	1213	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.3727	381	1213	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.3003	353	1213	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.2381	356	1213	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	77.9031	309	1213	95	below_threshold
Thauera terpenica	strain=58Eu	GCA_000443165.1	76113	76113	type	True	77.7394	310	1213	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.0986	217	1213	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.8236	199	1213	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:36,943] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34126/tc_result.tsv
[2023-03-15 13:21:36,944] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:36,944] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:36,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7876ee2b-e88b-4c7e-8c84-245f93a3c3af/dqc_reference/checkm_data
[2023-03-15 13:21:36,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:36,953] [INFO] Task started: CheckM
[2023-03-15 13:21:36,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34126/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34126/checkm_input OceanDNA-b34126/checkm_result
[2023-03-15 13:22:37,054] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:37,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:37,058] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:37,058] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:37,059] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34126/markers.fasta)
[2023-03-15 13:22:37,060] [INFO] Task started: Blastn
[2023-03-15 13:22:37,060] [INFO] Running command: blastn -query OceanDNA-b34126/markers.fasta -db /var/lib/cwl/stg7876ee2b-e88b-4c7e-8c84-245f93a3c3af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34126/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:38,528] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:38,530] [INFO] Selected 27 target genomes.
[2023-03-15 13:22:38,530] [INFO] Target genome list was writen to OceanDNA-b34126/target_genomes_gtdb.txt
[2023-03-15 13:22:38,579] [INFO] Task started: fastANI
[2023-03-15 13:22:38,579] [INFO] Running command: fastANI --query /var/lib/cwl/stge0cd44be-e7b8-477c-bc12-42c2a782c3a5/OceanDNA-b34126.fa --refList OceanDNA-b34126/target_genomes_gtdb.txt --output OceanDNA-b34126/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:58,178] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:58,193] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:22:58,193] [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_016177805.1	s__JACOUN01 sp016177805	79.2533	405	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACOUN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	78.9684	391	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911005.1	s__Aromatoleum toluolicum	78.8106	422	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156155.1	s__Aromatoleum tolulyticum	78.7754	427	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354895.1	s__Thauera sp002354895	78.7687	380	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	78.7633	401	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCF_012910705.1	s__Aromatoleum anaerobium	78.7093	402	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378245.1	s__Aromatoleum toluclasticum	78.709	446	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240785.1	s__Thauera sp018240785	78.6916	356	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801305.1	s__Thauera_A rhizosphaerae	78.6685	399	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910905.1	s__Aromatoleum toluvorans	78.664	423	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910885.1	s__Azoarcus_F taiwanensis	78.6349	374	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910785.1	s__Aromatoleum buckelii	78.6169	383	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017894385.1	s__Aromatoleum petrolei	78.5972	414	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001274695.1	s__Aromatoleum sp001274695	78.5841	402	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034845.1	s__Thauera_A sp003034845	78.5772	403	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017894365.1	s__Aromatoleum bremense	78.5746	417	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	99.97	99.97	1.00	1.00	2	-
GCF_014822185.1	s__Aromatoleum sp014822185	78.5547	433	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190925.1	s__Aromatoleum sp001190925	78.5264	413	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469595.1	s__Thauera sp009469595	78.5099	351	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422685.1	s__Thauera sp002422685	78.4989	361	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	78.4325	281	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_002872475.1	s__Azoarcus_D pumilus	78.4219	357	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801295.1	s__Thauera_A nasutitermitis	78.3728	381	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911595.1	s__Azoarcus_D sp013911595	78.3424	246	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295105.1	s__Thauera sp004295105	78.3393	347	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240585.1	s__Thauera sp018240585	78.16	329	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:58,194] [INFO] GTDB search result was written to OceanDNA-b34126/result_gtdb.tsv
[2023-03-15 13:22:58,195] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:58,198] [INFO] DFAST_QC result json was written to OceanDNA-b34126/dqc_result.json
[2023-03-15 13:22:58,198] [INFO] DFAST_QC completed!
[2023-03-15 13:22:58,198] [INFO] Total running time: 0h2m7s