[2024-01-24 13:55:46,135] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:46,137] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:46,138] [INFO] DQC Reference Directory: /var/lib/cwl/stgd996dbe4-0890-4589-b50d-d94f3297431b/dqc_reference
[2024-01-24 13:55:47,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:47,387] [INFO] Task started: Prodigal
[2024-01-24 13:55:47,388] [INFO] Running command: gunzip -c /var/lib/cwl/stgce978dae-e59f-4257-837c-dfed7fc244f3/GCF_000231385.2_ASM23138v3_genomic.fna.gz | prodigal -d GCF_000231385.2_ASM23138v3_genomic.fna/cds.fna -a GCF_000231385.2_ASM23138v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:58,285] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:58,286] [INFO] Task started: HMMsearch
[2024-01-24 13:55:58,286] [INFO] Running command: hmmsearch --tblout GCF_000231385.2_ASM23138v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd996dbe4-0890-4589-b50d-d94f3297431b/dqc_reference/reference_markers.hmm GCF_000231385.2_ASM23138v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:58,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:58,603] [INFO] Found 6/6 markers.
[2024-01-24 13:55:58,645] [INFO] Query marker FASTA was written to GCF_000231385.2_ASM23138v3_genomic.fna/markers.fasta
[2024-01-24 13:55:58,646] [INFO] Task started: Blastn
[2024-01-24 13:55:58,646] [INFO] Running command: blastn -query GCF_000231385.2_ASM23138v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgd996dbe4-0890-4589-b50d-d94f3297431b/dqc_reference/reference_markers.fasta -out GCF_000231385.2_ASM23138v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:59,217] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:59,221] [INFO] Selected 13 target genomes.
[2024-01-24 13:55:59,221] [INFO] Target genome list was writen to GCF_000231385.2_ASM23138v3_genomic.fna/target_genomes.txt
[2024-01-24 13:55:59,229] [INFO] Task started: fastANI
[2024-01-24 13:55:59,229] [INFO] Running command: fastANI --query /var/lib/cwl/stgce978dae-e59f-4257-837c-dfed7fc244f3/GCF_000231385.2_ASM23138v3_genomic.fna.gz --refList GCF_000231385.2_ASM23138v3_genomic.fna/target_genomes.txt --output GCF_000231385.2_ASM23138v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:10,445] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:10,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd996dbe4-0890-4589-b50d-d94f3297431b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:10,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd996dbe4-0890-4589-b50d-d94f3297431b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:10,461] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:10,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:10,462] [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 meridiei	strain=DSM 13257	GCA_000231385.3	79209	79209	type	True	100.0	1624	1624	95	conclusive
Desulfosporosinus hippei	strain=DSM 8344	GCA_900100785.1	569859	569859	type	True	94.237	1318	1624	95	below_threshold
Desulfosporosinus lacus	strain=DSM 15449	GCA_900129935.1	329936	329936	type	True	80.7068	790	1624	95	below_threshold
Desulfosporosinus youngiae	strain=DSM 17734	GCA_000244895.1	339862	339862	type	True	80.3739	642	1624	95	below_threshold
Desulfosporosinus orientis	strain=DSM 765	GCA_000235605.1	1563	1563	type	True	79.8295	569	1624	95	below_threshold
Desulfitobacterium metallireducens	strain=853-15A	GCA_000231405.3	142877	142877	type	True	78.9582	68	1624	95	below_threshold
Desulfosporosinus fructosivorans	strain=63.6F	GCA_004766045.1	2018669	2018669	type	True	78.807	392	1624	95	below_threshold
Desulfosporosinus acidiphilus	strain=SJ4	GCA_000255115.3	885581	885581	type	True	78.6863	192	1624	95	below_threshold
Desulfosporosinus metallidurans	strain=OL	GCA_001936615.1	1888891	1888891	type	True	77.4666	281	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:10,464] [INFO] DFAST Taxonomy check result was written to GCF_000231385.2_ASM23138v3_genomic.fna/tc_result.tsv
[2024-01-24 13:56:10,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:10,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:10,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd996dbe4-0890-4589-b50d-d94f3297431b/dqc_reference/checkm_data
[2024-01-24 13:56:10,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:10,510] [INFO] Task started: CheckM
[2024-01-24 13:56:10,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000231385.2_ASM23138v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000231385.2_ASM23138v3_genomic.fna/checkm_input GCF_000231385.2_ASM23138v3_genomic.fna/checkm_result
[2024-01-24 13:56:45,831] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:45,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:45,853] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:45,853] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:45,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000231385.2_ASM23138v3_genomic.fna/markers.fasta)
[2024-01-24 13:56:45,854] [INFO] Task started: Blastn
[2024-01-24 13:56:45,854] [INFO] Running command: blastn -query GCF_000231385.2_ASM23138v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgd996dbe4-0890-4589-b50d-d94f3297431b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000231385.2_ASM23138v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:46,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:46,578] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:46,578] [INFO] Target genome list was writen to GCF_000231385.2_ASM23138v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:46,588] [INFO] Task started: fastANI
[2024-01-24 13:56:46,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgce978dae-e59f-4257-837c-dfed7fc244f3/GCF_000231385.2_ASM23138v3_genomic.fna.gz --refList GCF_000231385.2_ASM23138v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000231385.2_ASM23138v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:57,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:57,310] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:57,310] [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_000231385.2	s__Desulfosporosinus meridiei	100.0	1624	1624	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_900100785.1	s__Desulfosporosinus hippei	94.2221	1319	1624	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_000765145.1	s__Desulfosporosinus sp000765145	92.7741	1198	1624	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_900129935.1	s__Desulfosporosinus lacus	80.7223	788	1624	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	80.4056	646	1624	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_000235605.1	s__Desulfosporosinus orientis	79.8137	572	1624	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_003513495.1	s__Desulfosporosinus sp003513495	79.6573	504	1624	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	98.30	98.26	0.84	0.84	3	-
GCF_000255115.2	s__Desulfosporosinus acidiphilus	78.6488	193	1624	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	78.5842	352	1624	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 13:56:57,312] [INFO] GTDB search result was written to GCF_000231385.2_ASM23138v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:57,313] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:57,316] [INFO] DFAST_QC result json was written to GCF_000231385.2_ASM23138v3_genomic.fna/dqc_result.json
[2024-01-24 13:56:57,316] [INFO] DFAST_QC completed!
[2024-01-24 13:56:57,316] [INFO] Total running time: 0h1m11s