[2024-01-24 13:45:41,014] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:41,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:41,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg98a59b5b-75c8-4920-8359-94c36b273181/dqc_reference
[2024-01-24 13:45:42,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:42,240] [INFO] Task started: Prodigal
[2024-01-24 13:45:42,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d926249-979e-48ea-9cff-1ad18c3879ca/GCF_017309585.1_ASM1730958v1_genomic.fna.gz | prodigal -d GCF_017309585.1_ASM1730958v1_genomic.fna/cds.fna -a GCF_017309585.1_ASM1730958v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:57,966] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:57,966] [INFO] Task started: HMMsearch
[2024-01-24 13:45:57,966] [INFO] Running command: hmmsearch --tblout GCF_017309585.1_ASM1730958v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98a59b5b-75c8-4920-8359-94c36b273181/dqc_reference/reference_markers.hmm GCF_017309585.1_ASM1730958v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:58,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:58,277] [INFO] Found 6/6 markers.
[2024-01-24 13:45:58,324] [INFO] Query marker FASTA was written to GCF_017309585.1_ASM1730958v1_genomic.fna/markers.fasta
[2024-01-24 13:45:58,325] [INFO] Task started: Blastn
[2024-01-24 13:45:58,325] [INFO] Running command: blastn -query GCF_017309585.1_ASM1730958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98a59b5b-75c8-4920-8359-94c36b273181/dqc_reference/reference_markers.fasta -out GCF_017309585.1_ASM1730958v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:59,245] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:59,254] [INFO] Selected 22 target genomes.
[2024-01-24 13:45:59,255] [INFO] Target genome list was writen to GCF_017309585.1_ASM1730958v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:59,269] [INFO] Task started: fastANI
[2024-01-24 13:45:59,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d926249-979e-48ea-9cff-1ad18c3879ca/GCF_017309585.1_ASM1730958v1_genomic.fna.gz --refList GCF_017309585.1_ASM1730958v1_genomic.fna/target_genomes.txt --output GCF_017309585.1_ASM1730958v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:17,194] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:17,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98a59b5b-75c8-4920-8359-94c36b273181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:17,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98a59b5b-75c8-4920-8359-94c36b273181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:17,210] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:17,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:17,211] [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 aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	100.0	1579	1581	95	conclusive
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	81.5786	848	1581	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.9128	390	1581	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.5659	336	1581	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	78.5496	316	1581	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.4224	379	1581	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	78.318	375	1581	95	below_threshold
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	78.2843	378	1581	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.2349	353	1581	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.9821	337	1581	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.98	346	1581	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	77.8208	338	1581	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.6364	244	1581	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	77.4249	246	1581	95	below_threshold
Cupriavidus campinensis	strain=LMG 19282	GCA_905397395.1	151783	151783	type	True	76.9046	179	1581	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	76.7334	121	1581	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	76.4386	122	1581	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	75.8589	116	1581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:17,212] [INFO] DFAST Taxonomy check result was written to GCF_017309585.1_ASM1730958v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:17,213] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:17,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:17,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98a59b5b-75c8-4920-8359-94c36b273181/dqc_reference/checkm_data
[2024-01-24 13:46:17,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:17,263] [INFO] Task started: CheckM
[2024-01-24 13:46:17,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017309585.1_ASM1730958v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017309585.1_ASM1730958v1_genomic.fna/checkm_input GCF_017309585.1_ASM1730958v1_genomic.fna/checkm_result
[2024-01-24 13:47:37,333] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:37,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:37,364] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:37,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:37,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017309585.1_ASM1730958v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:37,365] [INFO] Task started: Blastn
[2024-01-24 13:47:37,366] [INFO] Running command: blastn -query GCF_017309585.1_ASM1730958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98a59b5b-75c8-4920-8359-94c36b273181/dqc_reference/reference_markers_gtdb.fasta -out GCF_017309585.1_ASM1730958v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:39,053] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:39,057] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:39,058] [INFO] Target genome list was writen to GCF_017309585.1_ASM1730958v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:39,104] [INFO] Task started: fastANI
[2024-01-24 13:47:39,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d926249-979e-48ea-9cff-1ad18c3879ca/GCF_017309585.1_ASM1730958v1_genomic.fna.gz --refList GCF_017309585.1_ASM1730958v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017309585.1_ASM1730958v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:54,357] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:54,378] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:54,378] [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_017309585.1	s__Denitromonas sp017309585	100.0	1579	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	98.28	98.28	0.96	0.96	2	conclusive
GCF_010983895.1	s__Denitromonas sp010983895	81.6016	846	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018524365.1	s__Denitromonas sp018524365	79.882	663	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501585.1	s__Denitromonas sp008501585	79.7806	610	1581	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	79.3621	527	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	98.77	98.30	0.95	0.94	5	-
GCF_007625155.1	s__Denitromonas halophilus_A	79.2746	549	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489115.1	s__Thauera_A sp014489115	78.635	433	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	-
GCA_018240785.1	s__Thauera sp018240785	78.2511	343	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_001591165.1	s__Thauera butanivorans	78.2416	351	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	78.2217	355	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	78.0888	331	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_012911005.1	s__Aromatoleum toluolicum	77.98	346	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_900156155.1	s__Aromatoleum tolulyticum	77.8121	339	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_001274695.1	s__Aromatoleum sp001274695	77.6687	250	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_905397395.1	s__Cupriavidus campinensis	76.9034	178	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.28	95.05	0.89	0.86	6	-
GCF_002257565.1	s__Herbaspirillum sp002257565	76.3816	87	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009781175.1	s__Niveibacterium sp009781175	76.3422	119	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Niveibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:54,379] [INFO] GTDB search result was written to GCF_017309585.1_ASM1730958v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:54,380] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:54,384] [INFO] DFAST_QC result json was written to GCF_017309585.1_ASM1730958v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:54,384] [INFO] DFAST_QC completed!
[2024-01-24 13:47:54,384] [INFO] Total running time: 0h2m13s