[2024-01-24 11:58:20,271] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,273] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,273] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a4e794a-eac4-44ef-b8b2-ac2eb7f8995a/dqc_reference
[2024-01-24 11:58:21,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,493] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,494] [INFO] Running command: gunzip -c /var/lib/cwl/stg10ad450a-05a1-4695-a9d1-35cde4631a2f/GCF_017161445.1_ASM1716144v1_genomic.fna.gz | prodigal -d GCF_017161445.1_ASM1716144v1_genomic.fna/cds.fna -a GCF_017161445.1_ASM1716144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:37,731] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:37,731] [INFO] Task started: HMMsearch
[2024-01-24 11:58:37,731] [INFO] Running command: hmmsearch --tblout GCF_017161445.1_ASM1716144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a4e794a-eac4-44ef-b8b2-ac2eb7f8995a/dqc_reference/reference_markers.hmm GCF_017161445.1_ASM1716144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:38,033] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:38,035] [INFO] Found 6/6 markers.
[2024-01-24 11:58:38,080] [INFO] Query marker FASTA was written to GCF_017161445.1_ASM1716144v1_genomic.fna/markers.fasta
[2024-01-24 11:58:38,080] [INFO] Task started: Blastn
[2024-01-24 11:58:38,080] [INFO] Running command: blastn -query GCF_017161445.1_ASM1716144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a4e794a-eac4-44ef-b8b2-ac2eb7f8995a/dqc_reference/reference_markers.fasta -out GCF_017161445.1_ASM1716144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:38,960] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:38,965] [INFO] Selected 19 target genomes.
[2024-01-24 11:58:38,965] [INFO] Target genome list was writen to GCF_017161445.1_ASM1716144v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:38,978] [INFO] Task started: fastANI
[2024-01-24 11:58:38,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg10ad450a-05a1-4695-a9d1-35cde4631a2f/GCF_017161445.1_ASM1716144v1_genomic.fna.gz --refList GCF_017161445.1_ASM1716144v1_genomic.fna/target_genomes.txt --output GCF_017161445.1_ASM1716144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:55,620] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:55,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a4e794a-eac4-44ef-b8b2-ac2eb7f8995a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:55,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a4e794a-eac4-44ef-b8b2-ac2eb7f8995a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:55,646] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:58:55,647] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:58:55,647] [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
Niveibacterium microcysteis	strain=HC41	GCA_017161445.1	2811415	2811415	type	True	100.0	1614	1617	95	conclusive
Niveibacterium umoris	strain=KACC 17062	GCA_017311475.1	1193620	1193620	type	True	84.8944	1036	1617	95	below_threshold
Niveibacterium umoris	strain=DSM 106739	GCA_014197015.1	1193620	1193620	type	True	84.7504	1061	1617	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	78.4521	337	1617	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.4159	287	1617	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	78.3716	355	1617	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.3468	367	1617	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	78.3295	299	1617	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	78.243	366	1617	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	78.2377	287	1617	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.1559	370	1617	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	78.1153	351	1617	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	78.0892	298	1617	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	77.9941	368	1617	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	77.9659	301	1617	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	77.8981	363	1617	95	below_threshold
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	77.5373	350	1617	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.3598	257	1617	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.0275	245	1617	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:55,648] [INFO] DFAST Taxonomy check result was written to GCF_017161445.1_ASM1716144v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:55,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:55,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:55,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a4e794a-eac4-44ef-b8b2-ac2eb7f8995a/dqc_reference/checkm_data
[2024-01-24 11:58:55,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:55,694] [INFO] Task started: CheckM
[2024-01-24 11:58:55,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017161445.1_ASM1716144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017161445.1_ASM1716144v1_genomic.fna/checkm_input GCF_017161445.1_ASM1716144v1_genomic.fna/checkm_result
[2024-01-24 11:59:49,848] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:49,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 16.67%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:49,876] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:49,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:49,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017161445.1_ASM1716144v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:49,877] [INFO] Task started: Blastn
[2024-01-24 11:59:49,878] [INFO] Running command: blastn -query GCF_017161445.1_ASM1716144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a4e794a-eac4-44ef-b8b2-ac2eb7f8995a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017161445.1_ASM1716144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:51,468] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:51,473] [INFO] Selected 23 target genomes.
[2024-01-24 11:59:51,473] [INFO] Target genome list was writen to GCF_017161445.1_ASM1716144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:51,525] [INFO] Task started: fastANI
[2024-01-24 11:59:51,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg10ad450a-05a1-4695-a9d1-35cde4631a2f/GCF_017161445.1_ASM1716144v1_genomic.fna.gz --refList GCF_017161445.1_ASM1716144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017161445.1_ASM1716144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:08,599] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:08,623] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:08,624] [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_017161445.1	s__Niveibacterium microcysteis	100.0	1614	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Niveibacterium	95.0	97.91	97.91	0.91	0.91	2	conclusive
GCF_014197015.1	s__Niveibacterium umoris	84.7066	1066	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Niveibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003628555.1	s__Aromatoleum sp003628555	78.6381	348	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245655.1	s__Thauera propionica	78.45	337	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.06	98.06	0.86	0.86	2	-
GCF_014489115.1	s__Thauera_A sp014489115	78.449	365	1617	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_017894365.1	s__Aromatoleum bremense	78.4002	298	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001591165.1	s__Thauera butanivorans	78.3502	366	1617	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	78.3233	350	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025965.1	s__Aromatoleum aromaticum	78.2141	289	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	98.48	98.48	0.91	0.91	2	-
GCA_009781175.1	s__Niveibacterium sp009781175	78.177	281	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Niveibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539865.1	s__Zoogloea ramigera	78.1219	350	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	99.03	99.03	0.93	0.93	2	-
GCF_000378945.1	s__Methyloversatilis universalis_A	78.1195	315	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469605.1	s__Zoogloea sp009469605	78.0498	371	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274695.1	s__Aromatoleum sp001274695	78.0091	303	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801295.1	s__Thauera_A nasutitermitis	77.8862	366	1617	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_014736495.1	s__Dactylopiibacterium carminicum	77.821	237	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Dactylopiibacterium	95.0	99.96	99.89	0.99	0.97	4	-
GCA_017302295.1	s__Thauera sp017302295	77.8003	347	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911595.1	s__Azoarcus_D sp013911595	77.7567	182	1617	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_016789125.1	s__Zoogloea sp016789125	77.6227	282	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868295.1	s__Desulfobacillus sp016868295	77.5917	248	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927165.1	s__Zoogloea sp012927165	77.5479	349	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235765.1	s__Fen-999 sp016235765	77.4903	244	1617	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_905339315.1	s__Desulfobacillus sp905339315	77.0531	191	1617	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.66	96.66	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:08,626] [INFO] GTDB search result was written to GCF_017161445.1_ASM1716144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:08,627] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:08,634] [INFO] DFAST_QC result json was written to GCF_017161445.1_ASM1716144v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:08,635] [INFO] DFAST_QC completed!
[2024-01-24 12:00:08,635] [INFO] Total running time: 0h1m48s