[2024-01-25 20:14:50,349] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:50,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:50,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc021e37-fca6-4bab-b408-bb27c05f5854/dqc_reference
[2024-01-25 20:14:51,447] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:51,448] [INFO] Task started: Prodigal
[2024-01-25 20:14:51,448] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd8c28ee-fb02-49bb-8f55-b7844327b20b/GCF_000255115.2_ASM25511v3_genomic.fna.gz | prodigal -d GCF_000255115.2_ASM25511v3_genomic.fna/cds.fna -a GCF_000255115.2_ASM25511v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:01,012] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:01,012] [INFO] Task started: HMMsearch
[2024-01-25 20:15:01,013] [INFO] Running command: hmmsearch --tblout GCF_000255115.2_ASM25511v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc021e37-fca6-4bab-b408-bb27c05f5854/dqc_reference/reference_markers.hmm GCF_000255115.2_ASM25511v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:01,263] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:01,264] [INFO] Found 6/6 markers.
[2024-01-25 20:15:01,302] [INFO] Query marker FASTA was written to GCF_000255115.2_ASM25511v3_genomic.fna/markers.fasta
[2024-01-25 20:15:01,303] [INFO] Task started: Blastn
[2024-01-25 20:15:01,303] [INFO] Running command: blastn -query GCF_000255115.2_ASM25511v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc021e37-fca6-4bab-b408-bb27c05f5854/dqc_reference/reference_markers.fasta -out GCF_000255115.2_ASM25511v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:01,832] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:01,835] [INFO] Selected 11 target genomes.
[2024-01-25 20:15:01,835] [INFO] Target genome list was writen to GCF_000255115.2_ASM25511v3_genomic.fna/target_genomes.txt
[2024-01-25 20:15:01,839] [INFO] Task started: fastANI
[2024-01-25 20:15:01,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd8c28ee-fb02-49bb-8f55-b7844327b20b/GCF_000255115.2_ASM25511v3_genomic.fna.gz --refList GCF_000255115.2_ASM25511v3_genomic.fna/target_genomes.txt --output GCF_000255115.2_ASM25511v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:10,694] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:10,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc021e37-fca6-4bab-b408-bb27c05f5854/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:10,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc021e37-fca6-4bab-b408-bb27c05f5854/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:10,701] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:10,701] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:10,701] [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
Desulfosporosinus acidiphilus	strain=SJ4	GCA_000255115.3	885581	885581	type	True	100.0	1663	1663	95	conclusive
Desulfosporosinus acididurans	strain=M1	GCA_001029285.1	476652	476652	type	True	81.2462	807	1663	95	below_threshold
Desulfosporosinus meridiei	strain=DSM 13257	GCA_000231385.3	79209	79209	type	True	78.6018	185	1663	95	below_threshold
Desulfosporosinus hippei	strain=DSM 8344	GCA_900100785.1	569859	569859	type	True	77.5343	175	1663	95	below_threshold
Desulfosporosinus metallidurans	strain=OL	GCA_001936615.1	1888891	1888891	type	True	77.4577	239	1663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:10,703] [INFO] DFAST Taxonomy check result was written to GCF_000255115.2_ASM25511v3_genomic.fna/tc_result.tsv
[2024-01-25 20:15:10,703] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:10,703] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:10,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc021e37-fca6-4bab-b408-bb27c05f5854/dqc_reference/checkm_data
[2024-01-25 20:15:10,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:10,756] [INFO] Task started: CheckM
[2024-01-25 20:15:10,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000255115.2_ASM25511v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000255115.2_ASM25511v3_genomic.fna/checkm_input GCF_000255115.2_ASM25511v3_genomic.fna/checkm_result
[2024-01-25 20:15:42,418] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:42,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:42,440] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:42,440] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:42,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000255115.2_ASM25511v3_genomic.fna/markers.fasta)
[2024-01-25 20:15:42,440] [INFO] Task started: Blastn
[2024-01-25 20:15:42,441] [INFO] Running command: blastn -query GCF_000255115.2_ASM25511v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc021e37-fca6-4bab-b408-bb27c05f5854/dqc_reference/reference_markers_gtdb.fasta -out GCF_000255115.2_ASM25511v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:43,208] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:43,211] [INFO] Selected 15 target genomes.
[2024-01-25 20:15:43,212] [INFO] Target genome list was writen to GCF_000255115.2_ASM25511v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:43,224] [INFO] Task started: fastANI
[2024-01-25 20:15:43,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd8c28ee-fb02-49bb-8f55-b7844327b20b/GCF_000255115.2_ASM25511v3_genomic.fna.gz --refList GCF_000255115.2_ASM25511v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000255115.2_ASM25511v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:55,885] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:55,892] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:55,892] [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_000255115.2	s__Desulfosporosinus acidiphilus	100.0	1663	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001029285.1	s__Desulfosporosinus acididurans	81.2682	808	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	96.53	96.53	0.82	0.82	2	-
GCF_002196705.1	s__Desulfosporosinus sp002196705	81.1873	849	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000231385.2	s__Desulfosporosinus meridiei	78.6136	184	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000244895.1	s__Desulfosporosinus youngiae	78.4055	211	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004766055.1	s__Desulfosporosinus sp004766055	77.687	205	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100785.1	s__Desulfosporosinus hippei	77.5596	173	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000770645.1	s__Desulfosporosinus sp000770645	77.4343	94	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	99.63	99.30	0.85	0.80	5	-
GCA_000961805.1	s__Desulfosporosinus sp000961805	77.4257	219	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	99.79	99.68	0.91	0.86	3	-
GCA_001516045.1	s__Desulfosporosinus sp001516045	77.3374	181	1663	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:55,894] [INFO] GTDB search result was written to GCF_000255115.2_ASM25511v3_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:55,894] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:55,897] [INFO] DFAST_QC result json was written to GCF_000255115.2_ASM25511v3_genomic.fna/dqc_result.json
[2024-01-25 20:15:55,897] [INFO] DFAST_QC completed!
[2024-01-25 20:15:55,897] [INFO] Total running time: 0h1m6s