[2024-01-24 13:17:33,070] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:33,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:33,073] [INFO] DQC Reference Directory: /var/lib/cwl/stgc98172f6-d7ab-4fb1-9b7f-1b5bd846dd23/dqc_reference
[2024-01-24 13:17:34,478] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:34,481] [INFO] Task started: Prodigal
[2024-01-24 13:17:34,482] [INFO] Running command: gunzip -c /var/lib/cwl/stgb78529e1-e1c5-4799-a3ef-8913e94ee61a/GCF_012910815.1_ASM1291081v1_genomic.fna.gz | prodigal -d GCF_012910815.1_ASM1291081v1_genomic.fna/cds.fna -a GCF_012910815.1_ASM1291081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:50,599] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:50,600] [INFO] Task started: HMMsearch
[2024-01-24 13:17:50,600] [INFO] Running command: hmmsearch --tblout GCF_012910815.1_ASM1291081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc98172f6-d7ab-4fb1-9b7f-1b5bd846dd23/dqc_reference/reference_markers.hmm GCF_012910815.1_ASM1291081v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:50,949] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:50,950] [INFO] Found 6/6 markers.
[2024-01-24 13:17:50,994] [INFO] Query marker FASTA was written to GCF_012910815.1_ASM1291081v1_genomic.fna/markers.fasta
[2024-01-24 13:17:50,994] [INFO] Task started: Blastn
[2024-01-24 13:17:50,995] [INFO] Running command: blastn -query GCF_012910815.1_ASM1291081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc98172f6-d7ab-4fb1-9b7f-1b5bd846dd23/dqc_reference/reference_markers.fasta -out GCF_012910815.1_ASM1291081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:51,909] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:51,913] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:51,913] [INFO] Target genome list was writen to GCF_012910815.1_ASM1291081v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:51,916] [INFO] Task started: fastANI
[2024-01-24 13:17:51,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgb78529e1-e1c5-4799-a3ef-8913e94ee61a/GCF_012910815.1_ASM1291081v1_genomic.fna.gz --refList GCF_012910815.1_ASM1291081v1_genomic.fna/target_genomes.txt --output GCF_012910815.1_ASM1291081v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:06,395] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:06,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc98172f6-d7ab-4fb1-9b7f-1b5bd846dd23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:06,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc98172f6-d7ab-4fb1-9b7f-1b5bd846dd23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:06,410] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:06,411] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:06,411] [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
Azoarcus communis	strain=SWub3	GCA_012910815.1	41977	41977	type	True	100.0	1577	1581	95	conclusive
Azoarcus communis	strain=SWub3	GCA_003226565.1	41977	41977	type	True	99.9918	1577	1581	95	conclusive
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	80.4676	551	1581	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	80.4269	600	1581	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	80.2689	584	1581	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	79.8355	484	1581	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	79.7	491	1581	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	79.669	483	1581	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	79.654	616	1581	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	79.6314	617	1581	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.0334	453	1581	95	below_threshold
Aromatoleum diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	78.9668	424	1581	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.7356	380	1581	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.6886	390	1581	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.4335	381	1581	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.0373	323	1581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:06,413] [INFO] DFAST Taxonomy check result was written to GCF_012910815.1_ASM1291081v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:06,413] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:06,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:06,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc98172f6-d7ab-4fb1-9b7f-1b5bd846dd23/dqc_reference/checkm_data
[2024-01-24 13:18:06,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:06,468] [INFO] Task started: CheckM
[2024-01-24 13:18:06,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012910815.1_ASM1291081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012910815.1_ASM1291081v1_genomic.fna/checkm_input GCF_012910815.1_ASM1291081v1_genomic.fna/checkm_result
[2024-01-24 13:19:03,415] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:03,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:03,442] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:03,442] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:03,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012910815.1_ASM1291081v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:03,443] [INFO] Task started: Blastn
[2024-01-24 13:19:03,443] [INFO] Running command: blastn -query GCF_012910815.1_ASM1291081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc98172f6-d7ab-4fb1-9b7f-1b5bd846dd23/dqc_reference/reference_markers_gtdb.fasta -out GCF_012910815.1_ASM1291081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:05,095] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:05,099] [INFO] Selected 17 target genomes.
[2024-01-24 13:19:05,100] [INFO] Target genome list was writen to GCF_012910815.1_ASM1291081v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:05,134] [INFO] Task started: fastANI
[2024-01-24 13:19:05,134] [INFO] Running command: fastANI --query /var/lib/cwl/stgb78529e1-e1c5-4799-a3ef-8913e94ee61a/GCF_012910815.1_ASM1291081v1_genomic.fna.gz --refList GCF_012910815.1_ASM1291081v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012910815.1_ASM1291081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:20,221] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:20,235] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:20,236] [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_003226565.1	s__Azoarcus_C communis	99.9918	1577	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	99.33	98.67	0.90	0.80	3	conclusive
GCF_003111645.1	s__Azoarcus_C communis_A	80.5426	716	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	97.65	97.63	0.87	0.87	3	-
GCF_002245655.1	s__Thauera propionica	80.4607	552	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.06	98.06	0.86	0.86	2	-
GCF_018122735.1	s__Azoarcus_C sp018122735	80.4516	675	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001051995.2	s__Thauera humireducens	80.4307	601	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
GCF_003111665.1	s__Azoarcus_C communis_B	80.3689	712	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	98.41	98.41	0.92	0.92	2	-
GCF_000310145.2	s__Thauera sp000310145	80.3534	561	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.71	98.54	0.88	0.86	4	-
GCF_001682385.1	s__Azoarcus olearius	80.2827	659	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	98.77	98.77	0.96	0.96	2	-
GCF_001591165.1	s__Thauera butanivorans	80.2727	584	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310205.1	s__Thauera linaloolentis	80.1056	495	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014489115.1	s__Thauera_A sp014489115	80.071	577	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002354895.1	s__Thauera sp002354895	80.0188	547	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469595.1	s__Thauera sp009469595	79.983	544	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240785.1	s__Thauera sp018240785	79.9572	548	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030465.1	s__Thauera aromatica	79.694	492	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910705.1	s__Aromatoleum anaerobium	78.7242	375	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910785.1	s__Aromatoleum buckelii	78.3515	389	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:20,237] [INFO] GTDB search result was written to GCF_012910815.1_ASM1291081v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:20,238] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:20,244] [INFO] DFAST_QC result json was written to GCF_012910815.1_ASM1291081v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:20,245] [INFO] DFAST_QC completed!
[2024-01-24 13:19:20,245] [INFO] Total running time: 0h1m47s