[2024-01-24 12:45:10,400] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,401] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a9fc7ce-4e8b-4c2a-b4a9-f21a74c5b765/dqc_reference
[2024-01-24 12:45:13,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,082] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgcee82546-3d84-4df9-90ed-b57a9458131f/GCF_009380135.2_ASM938013v2_genomic.fna.gz | prodigal -d GCF_009380135.2_ASM938013v2_genomic.fna/cds.fna -a GCF_009380135.2_ASM938013v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:27,599] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:27,599] [INFO] Task started: HMMsearch
[2024-01-24 12:45:27,599] [INFO] Running command: hmmsearch --tblout GCF_009380135.2_ASM938013v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a9fc7ce-4e8b-4c2a-b4a9-f21a74c5b765/dqc_reference/reference_markers.hmm GCF_009380135.2_ASM938013v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:27,879] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:27,880] [INFO] Found 6/6 markers.
[2024-01-24 12:45:27,920] [INFO] Query marker FASTA was written to GCF_009380135.2_ASM938013v2_genomic.fna/markers.fasta
[2024-01-24 12:45:27,921] [INFO] Task started: Blastn
[2024-01-24 12:45:27,921] [INFO] Running command: blastn -query GCF_009380135.2_ASM938013v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a9fc7ce-4e8b-4c2a-b4a9-f21a74c5b765/dqc_reference/reference_markers.fasta -out GCF_009380135.2_ASM938013v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:28,892] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:28,895] [INFO] Selected 17 target genomes.
[2024-01-24 12:45:28,896] [INFO] Target genome list was writen to GCF_009380135.2_ASM938013v2_genomic.fna/target_genomes.txt
[2024-01-24 12:45:28,902] [INFO] Task started: fastANI
[2024-01-24 12:45:28,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgcee82546-3d84-4df9-90ed-b57a9458131f/GCF_009380135.2_ASM938013v2_genomic.fna.gz --refList GCF_009380135.2_ASM938013v2_genomic.fna/target_genomes.txt --output GCF_009380135.2_ASM938013v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:43,160] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:43,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a9fc7ce-4e8b-4c2a-b4a9-f21a74c5b765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:43,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a9fc7ce-4e8b-4c2a-b4a9-f21a74c5b765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:43,175] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:43,175] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:43,175] [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
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	80.5679	700	1426	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	80.4941	751	1426	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	80.3145	745	1426	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	80.101	679	1426	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.8169	605	1426	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	79.7417	706	1426	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	79.6956	666	1426	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.481	642	1426	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.4625	644	1426	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.451	665	1426	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.4152	706	1426	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.3783	620	1426	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	79.1671	587	1426	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.9933	639	1426	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.9835	508	1426	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	78.4113	570	1426	95	below_threshold
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	77.702	399	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:43,177] [INFO] DFAST Taxonomy check result was written to GCF_009380135.2_ASM938013v2_genomic.fna/tc_result.tsv
[2024-01-24 12:45:43,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:43,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:43,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a9fc7ce-4e8b-4c2a-b4a9-f21a74c5b765/dqc_reference/checkm_data
[2024-01-24 12:45:43,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:43,220] [INFO] Task started: CheckM
[2024-01-24 12:45:43,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009380135.2_ASM938013v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009380135.2_ASM938013v2_genomic.fna/checkm_input GCF_009380135.2_ASM938013v2_genomic.fna/checkm_result
[2024-01-24 12:46:39,802] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:39,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:39,827] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:39,827] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:39,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009380135.2_ASM938013v2_genomic.fna/markers.fasta)
[2024-01-24 12:46:39,828] [INFO] Task started: Blastn
[2024-01-24 12:46:39,829] [INFO] Running command: blastn -query GCF_009380135.2_ASM938013v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a9fc7ce-4e8b-4c2a-b4a9-f21a74c5b765/dqc_reference/reference_markers_gtdb.fasta -out GCF_009380135.2_ASM938013v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:41,651] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:41,656] [INFO] Selected 19 target genomes.
[2024-01-24 12:46:41,656] [INFO] Target genome list was writen to GCF_009380135.2_ASM938013v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:41,677] [INFO] Task started: fastANI
[2024-01-24 12:46:41,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgcee82546-3d84-4df9-90ed-b57a9458131f/GCF_009380135.2_ASM938013v2_genomic.fna.gz --refList GCF_009380135.2_ASM938013v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009380135.2_ASM938013v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:57,824] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:57,855] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:57,855] [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_009380135.2	s__Fertoeibacter niger	100.0	1424	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000176015.1	s__Pseudorhodobacter_B sp000176015	80.7309	704	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	80.5773	699	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_900110025.1	s__Gemmobacter aquatilis	80.4213	744	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	80.3157	744	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008271655.1	s__Gemmobacter caeruleus	80.1277	675	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	79.8934	595	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297695.1	s__Rhodobacter_F sp013297695	79.7583	578	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	79.7514	707	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745575.1	s__ETT8 sp004745575	79.6957	666	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	97.69	97.69	0.90	0.90	2	-
GCF_009908315.1	s__Gemmobacter_B sp009908315	79.4293	668	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765775.1	s__Pseudorhodobacter sp016765775	79.4032	638	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570715.1	s__Gemmobacter lutimaris	79.394	709	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243445.1	s__Gemmobacter_B straminiformis	79.3783	620	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824045.1	s__Gemmobacter_B sp013824045	79.1441	464	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124615.1	s__Solirhodobacter sp016124615	79.14	627	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773375.1	s__Cypionkella sp009773375	78.9666	595	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407205.1	s__Cereibacter_A sp002407205	78.9267	587	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869835.1	s__KMS-5 sp016869835	78.8443	498	1426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:57,857] [INFO] GTDB search result was written to GCF_009380135.2_ASM938013v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:57,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:57,863] [INFO] DFAST_QC result json was written to GCF_009380135.2_ASM938013v2_genomic.fna/dqc_result.json
[2024-01-24 12:46:57,864] [INFO] DFAST_QC completed!
[2024-01-24 12:46:57,864] [INFO] Total running time: 0h1m47s