[2024-01-24 12:21:44,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cc7be92-75bd-4689-8476-0e3318b98cfb/dqc_reference
[2024-01-24 12:21:45,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,573] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,573] [INFO] Running command: gunzip -c /var/lib/cwl/stgee0ee3ba-6f8a-4721-b0fa-e3c4b08798e8/GCF_007830175.1_ASM783017v1_genomic.fna.gz | prodigal -d GCF_007830175.1_ASM783017v1_genomic.fna/cds.fna -a GCF_007830175.1_ASM783017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:54,579] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:54,579] [INFO] Task started: HMMsearch
[2024-01-24 12:21:54,579] [INFO] Running command: hmmsearch --tblout GCF_007830175.1_ASM783017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cc7be92-75bd-4689-8476-0e3318b98cfb/dqc_reference/reference_markers.hmm GCF_007830175.1_ASM783017v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:54,958] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:54,959] [INFO] Found 6/6 markers.
[2024-01-24 12:21:54,997] [INFO] Query marker FASTA was written to GCF_007830175.1_ASM783017v1_genomic.fna/markers.fasta
[2024-01-24 12:21:54,997] [INFO] Task started: Blastn
[2024-01-24 12:21:54,998] [INFO] Running command: blastn -query GCF_007830175.1_ASM783017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cc7be92-75bd-4689-8476-0e3318b98cfb/dqc_reference/reference_markers.fasta -out GCF_007830175.1_ASM783017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:55,663] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:55,666] [INFO] Selected 19 target genomes.
[2024-01-24 12:21:55,666] [INFO] Target genome list was writen to GCF_007830175.1_ASM783017v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:55,673] [INFO] Task started: fastANI
[2024-01-24 12:21:55,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgee0ee3ba-6f8a-4721-b0fa-e3c4b08798e8/GCF_007830175.1_ASM783017v1_genomic.fna.gz --refList GCF_007830175.1_ASM783017v1_genomic.fna/target_genomes.txt --output GCF_007830175.1_ASM783017v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:08,579] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:08,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cc7be92-75bd-4689-8476-0e3318b98cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:08,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cc7be92-75bd-4689-8476-0e3318b98cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:08,585] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:08,585] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:08,585] [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
Sedimentibacter saalensis	strain=DSM 13558	GCA_007830175.1	130788	130788	type	True	100.0	1267	1268	95	conclusive
Sedimentibacter acidaminivorans	strain=DSM 24004	GCA_017873955.1	913099	913099	type	True	77.5726	191	1268	95	below_threshold
Sedimentibacter hydroxybenzoicus	strain=DSM 7310	GCA_013403245.1	29345	29345	type	True	77.5254	248	1268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:08,587] [INFO] DFAST Taxonomy check result was written to GCF_007830175.1_ASM783017v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:08,587] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:08,587] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:08,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cc7be92-75bd-4689-8476-0e3318b98cfb/dqc_reference/checkm_data
[2024-01-24 12:22:08,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:08,627] [INFO] Task started: CheckM
[2024-01-24 12:22:08,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830175.1_ASM783017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830175.1_ASM783017v1_genomic.fna/checkm_input GCF_007830175.1_ASM783017v1_genomic.fna/checkm_result
[2024-01-24 12:22:40,350] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:40,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:40,374] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:40,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:40,375] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830175.1_ASM783017v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:40,376] [INFO] Task started: Blastn
[2024-01-24 12:22:40,376] [INFO] Running command: blastn -query GCF_007830175.1_ASM783017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cc7be92-75bd-4689-8476-0e3318b98cfb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830175.1_ASM783017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:41,446] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:41,450] [INFO] Selected 20 target genomes.
[2024-01-24 12:22:41,450] [INFO] Target genome list was writen to GCF_007830175.1_ASM783017v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:41,495] [INFO] Task started: fastANI
[2024-01-24 12:22:41,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgee0ee3ba-6f8a-4721-b0fa-e3c4b08798e8/GCF_007830175.1_ASM783017v1_genomic.fna.gz --refList GCF_007830175.1_ASM783017v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830175.1_ASM783017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:52,739] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:52,752] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:52,753] [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_007830175.1	s__Sedimentibacter saalensis	100.0	1267	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002422545.1	s__Sedimentibacter sp002422545	91.4525	957	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002381185.1	s__Sedimentibacter sp002381185	78.4501	372	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	99.05	98.81	0.89	0.88	6	-
GCA_002340985.1	s__Sedimentibacter sp002340985	77.9271	260	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	98.14	96.44	0.86	0.81	4	-
GCA_003457065.1	s__Sedimentibacter sp003457065	77.846	239	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	98.22	98.22	0.78	0.78	2	-
GCA_003497505.1	s__Sedimentibacter sp003497505	77.8097	190	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873955.1	s__Sedimentibacter acidaminivorans	77.617	192	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403245.1	s__Sedimentibacter hydroxybenzoicus	77.5378	247	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995755.1	s__Sedimentibacter sp017995755	77.1915	122	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519555.1	s__Sedimentibacter sp012519555	77.1561	150	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483345.1	s__Sedimentibacter sp003483345	77.0482	135	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	97.32	97.20	0.62	0.58	3	-
GCA_002399975.1	s__Sedimentibacter sp002399975	76.9004	165	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002332905.1	s__UBA1535 sp002332905	76.7593	50	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479485.1	s__UBA1535 sp002479485	76.5361	60	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	98.88	98.88	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:52,754] [INFO] GTDB search result was written to GCF_007830175.1_ASM783017v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:52,755] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:52,758] [INFO] DFAST_QC result json was written to GCF_007830175.1_ASM783017v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:52,758] [INFO] DFAST_QC completed!
[2024-01-24 12:22:52,758] [INFO] Total running time: 0h1m9s