[2024-01-24 10:47:40,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg65617232-db7e-432a-97fc-93cb4fe6bb96/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgf757751e-6781-44aa-bfac-592927171439/GCF_001936615.1_ASM193661v1_genomic.fna.gz | prodigal -d GCF_001936615.1_ASM193661v1_genomic.fna/cds.fna -a GCF_001936615.1_ASM193661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:56,498] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:56,499] [INFO] Task started: HMMsearch
[2024-01-24 10:47:56,499] [INFO] Running command: hmmsearch --tblout GCF_001936615.1_ASM193661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65617232-db7e-432a-97fc-93cb4fe6bb96/dqc_reference/reference_markers.hmm GCF_001936615.1_ASM193661v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:56,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:56,840] [INFO] Found 6/6 markers.
[2024-01-24 10:47:56,882] [INFO] Query marker FASTA was written to GCF_001936615.1_ASM193661v1_genomic.fna/markers.fasta
[2024-01-24 10:47:56,883] [INFO] Task started: Blastn
[2024-01-24 10:47:56,883] [INFO] Running command: blastn -query GCF_001936615.1_ASM193661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65617232-db7e-432a-97fc-93cb4fe6bb96/dqc_reference/reference_markers.fasta -out GCF_001936615.1_ASM193661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:57,449] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:57,453] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:57,453] [INFO] Target genome list was writen to GCF_001936615.1_ASM193661v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:57,482] [INFO] Task started: fastANI
[2024-01-24 10:47:57,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgf757751e-6781-44aa-bfac-592927171439/GCF_001936615.1_ASM193661v1_genomic.fna.gz --refList GCF_001936615.1_ASM193661v1_genomic.fna/target_genomes.txt --output GCF_001936615.1_ASM193661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:08,142] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:08,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65617232-db7e-432a-97fc-93cb4fe6bb96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:08,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65617232-db7e-432a-97fc-93cb4fe6bb96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:08,151] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:08,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:08,152] [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 metallidurans	strain=OL	GCA_001936615.1	1888891	1888891	type	True	100.0	1665	1668	95	conclusive
Desulfosporosinus fructosivorans	strain=63.6F	GCA_004766045.1	2018669	2018669	type	True	79.5953	615	1668	95	below_threshold
Desulfosporosinus lacus	strain=DSM 15449	GCA_900129935.1	329936	329936	type	True	78.9136	494	1668	95	below_threshold
Desulfosporosinus youngiae	strain=DSM 17734	GCA_000244895.1	339862	339862	type	True	77.8887	400	1668	95	below_threshold
Desulfosporosinus orientis	strain=DSM 765	GCA_000235605.1	1563	1563	type	True	77.8668	286	1668	95	below_threshold
Desulfosporosinus hippei	strain=DSM 8344	GCA_900100785.1	569859	569859	type	True	77.8355	295	1668	95	below_threshold
Desulfosporosinus acidiphilus	strain=SJ4	GCA_000255115.3	885581	885581	type	True	77.6386	221	1668	95	below_threshold
Desulfosporosinus meridiei	strain=DSM 13257	GCA_000231385.3	79209	79209	type	True	77.5577	283	1668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:08,153] [INFO] DFAST Taxonomy check result was written to GCF_001936615.1_ASM193661v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:08,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:08,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:08,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65617232-db7e-432a-97fc-93cb4fe6bb96/dqc_reference/checkm_data
[2024-01-24 10:48:08,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:08,210] [INFO] Task started: CheckM
[2024-01-24 10:48:08,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001936615.1_ASM193661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001936615.1_ASM193661v1_genomic.fna/checkm_input GCF_001936615.1_ASM193661v1_genomic.fna/checkm_result
[2024-01-24 10:48:47,318] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:47,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:47,341] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:47,341] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:47,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001936615.1_ASM193661v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:47,342] [INFO] Task started: Blastn
[2024-01-24 10:48:47,342] [INFO] Running command: blastn -query GCF_001936615.1_ASM193661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65617232-db7e-432a-97fc-93cb4fe6bb96/dqc_reference/reference_markers_gtdb.fasta -out GCF_001936615.1_ASM193661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:48,140] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:48,144] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:48,144] [INFO] Target genome list was writen to GCF_001936615.1_ASM193661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:48,170] [INFO] Task started: fastANI
[2024-01-24 10:48:48,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgf757751e-6781-44aa-bfac-592927171439/GCF_001936615.1_ASM193661v1_genomic.fna.gz --refList GCF_001936615.1_ASM193661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001936615.1_ASM193661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:01,486] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:01,506] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:01,506] [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_001936615.1	s__Desulfosporosinus sp001936615	100.0	1665	1668	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_004766055.1	s__Desulfosporosinus sp004766055	80.5694	630	1668	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_001707885.1	s__Desulfosporosinus sp001707885	80.5031	596	1668	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_000224515.1	s__Desulfosporosinus sp000224515	80.4145	616	1668	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_000961805.1	s__Desulfosporosinus sp000961805	80.222	579	1668	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	80.1101	589	1668	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_004766045.1	s__Desulfosporosinus fructosivorans	79.6214	611	1668	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_002404215.1	s__Desulfosporosinus sp002404215	79.4859	417	1668	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	79.0099	294	1668	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	99.63	99.30	0.85	0.80	5	-
GCF_900129935.1	s__Desulfosporosinus lacus	78.9174	493	1668	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_016278585.1	s__Desulfosporosinus sp016278585	78.2947	341	1668	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	77.8517	293	1668	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:01,508] [INFO] GTDB search result was written to GCF_001936615.1_ASM193661v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:01,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:01,512] [INFO] DFAST_QC result json was written to GCF_001936615.1_ASM193661v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:01,512] [INFO] DFAST_QC completed!
[2024-01-24 10:49:01,512] [INFO] Total running time: 0h1m21s