[2024-01-25 19:11:05,773] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:05,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:05,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg0722fecc-a091-48b3-9b2b-55965847d161/dqc_reference
[2024-01-25 19:11:06,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:06,931] [INFO] Task started: Prodigal
[2024-01-25 19:11:06,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e1c0d21-40d2-46a9-851a-9526b97f9f4e/GCF_010983895.1_ASM1098389v1_genomic.fna.gz | prodigal -d GCF_010983895.1_ASM1098389v1_genomic.fna/cds.fna -a GCF_010983895.1_ASM1098389v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:19,691] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:19,691] [INFO] Task started: HMMsearch
[2024-01-25 19:11:19,691] [INFO] Running command: hmmsearch --tblout GCF_010983895.1_ASM1098389v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0722fecc-a091-48b3-9b2b-55965847d161/dqc_reference/reference_markers.hmm GCF_010983895.1_ASM1098389v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:19,933] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:19,934] [INFO] Found 6/6 markers.
[2024-01-25 19:11:19,983] [INFO] Query marker FASTA was written to GCF_010983895.1_ASM1098389v1_genomic.fna/markers.fasta
[2024-01-25 19:11:19,984] [INFO] Task started: Blastn
[2024-01-25 19:11:19,984] [INFO] Running command: blastn -query GCF_010983895.1_ASM1098389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0722fecc-a091-48b3-9b2b-55965847d161/dqc_reference/reference_markers.fasta -out GCF_010983895.1_ASM1098389v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:20,936] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:20,939] [INFO] Selected 17 target genomes.
[2024-01-25 19:11:20,939] [INFO] Target genome list was writen to GCF_010983895.1_ASM1098389v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:20,970] [INFO] Task started: fastANI
[2024-01-25 19:11:20,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e1c0d21-40d2-46a9-851a-9526b97f9f4e/GCF_010983895.1_ASM1098389v1_genomic.fna.gz --refList GCF_010983895.1_ASM1098389v1_genomic.fna/target_genomes.txt --output GCF_010983895.1_ASM1098389v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:35,860] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:35,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0722fecc-a091-48b3-9b2b-55965847d161/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:35,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0722fecc-a091-48b3-9b2b-55965847d161/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:35,871] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:11:35,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:35,872] [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
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	100.0	1411	1412	95	conclusive
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	81.6618	850	1412	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	80.11	601	1412	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	80.0599	501	1412	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	80.0397	549	1412	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	79.7756	505	1412	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.5844	521	1412	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	79.3265	543	1412	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	79.2963	539	1412	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	79.2456	488	1412	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.0982	506	1412	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	79.0178	507	1412	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	78.87	497	1412	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	78.5148	411	1412	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.4491	390	1412	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	78.4374	405	1412	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.4128	436	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:35,873] [INFO] DFAST Taxonomy check result was written to GCF_010983895.1_ASM1098389v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:35,873] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:35,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:35,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0722fecc-a091-48b3-9b2b-55965847d161/dqc_reference/checkm_data
[2024-01-25 19:11:35,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:35,915] [INFO] Task started: CheckM
[2024-01-25 19:11:35,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010983895.1_ASM1098389v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010983895.1_ASM1098389v1_genomic.fna/checkm_input GCF_010983895.1_ASM1098389v1_genomic.fna/checkm_result
[2024-01-25 19:13:08,495] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:08,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:08,527] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:08,527] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:08,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010983895.1_ASM1098389v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:08,528] [INFO] Task started: Blastn
[2024-01-25 19:13:08,528] [INFO] Running command: blastn -query GCF_010983895.1_ASM1098389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0722fecc-a091-48b3-9b2b-55965847d161/dqc_reference/reference_markers_gtdb.fasta -out GCF_010983895.1_ASM1098389v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:10,505] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:10,509] [INFO] Selected 14 target genomes.
[2024-01-25 19:13:10,509] [INFO] Target genome list was writen to GCF_010983895.1_ASM1098389v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:10,529] [INFO] Task started: fastANI
[2024-01-25 19:13:10,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e1c0d21-40d2-46a9-851a-9526b97f9f4e/GCF_010983895.1_ASM1098389v1_genomic.fna.gz --refList GCF_010983895.1_ASM1098389v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010983895.1_ASM1098389v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:24,184] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:24,196] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:24,196] [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_010983895.1	s__Denitromonas sp010983895	100.0	1412	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018524365.1	s__Denitromonas sp018524365	82.0027	827	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309585.1	s__Denitromonas sp017309585	81.6804	851	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	98.28	98.28	0.96	0.96	2	-
GCA_008501585.1	s__Denitromonas sp008501585	81.6395	789	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007625205.1	s__Denitromonas halophilus	80.256	704	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	98.77	98.30	0.95	0.94	5	-
GCF_014489115.1	s__Thauera_A sp014489115	80.1483	654	1412	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_004801305.1	s__Thauera_A rhizosphaerae	80.0972	603	1412	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_000310225.1	s__Thauera phenylacetica	80.0832	499	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469605.1	s__Zoogloea sp009469605	79.2875	578	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361735.1	s__Azoarcus indigens	79.2762	549	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012910905.1	s__Aromatoleum toluvorans	79.0263	506	1412	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	79.0234	494	1412	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	78.8577	500	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274695.1	s__Aromatoleum sp001274695	78.3196	395	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:24,197] [INFO] GTDB search result was written to GCF_010983895.1_ASM1098389v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:24,200] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:24,204] [INFO] DFAST_QC result json was written to GCF_010983895.1_ASM1098389v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:24,204] [INFO] DFAST_QC completed!
[2024-01-25 19:13:24,204] [INFO] Total running time: 0h2m18s