[2024-01-24 13:22:02,291] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,293] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,293] [INFO] DQC Reference Directory: /var/lib/cwl/stg33494787-caf9-486d-86dd-4c8305dbe12e/dqc_reference
[2024-01-24 13:22:03,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,674] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e80f21c-43e8-4a0c-8e17-07213f8c9b05/GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/cds.fna -a GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:16,450] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:16,451] [INFO] Task started: HMMsearch
[2024-01-24 13:22:16,451] [INFO] Running command: hmmsearch --tblout GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33494787-caf9-486d-86dd-4c8305dbe12e/dqc_reference/reference_markers.hmm GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:16,813] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:16,814] [INFO] Found 6/6 markers.
[2024-01-24 13:22:16,866] [INFO] Query marker FASTA was written to GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:16,866] [INFO] Task started: Blastn
[2024-01-24 13:22:16,866] [INFO] Running command: blastn -query GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg33494787-caf9-486d-86dd-4c8305dbe12e/dqc_reference/reference_markers.fasta -out GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:17,519] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:17,522] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:17,523] [INFO] Target genome list was writen to GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:17,530] [INFO] Task started: fastANI
[2024-01-24 13:22:17,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e80f21c-43e8-4a0c-8e17-07213f8c9b05/GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna.gz --refList GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:27,878] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:27,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33494787-caf9-486d-86dd-4c8305dbe12e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:27,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33494787-caf9-486d-86dd-4c8305dbe12e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:27,886] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:27,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:27,886] [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
Sporomusa malonica	strain=DSM 5090	GCA_900176355.1	112901	112901	type	True	100.0	1690	1695	95	conclusive
Sporomusa silvacetica	strain=DSM 10669	GCA_002257705.1	55504	55504	type	True	79.4897	527	1695	95	below_threshold
Sporomusa sphaeroides	strain=DSM 2875	GCA_023660125.1	47679	47679	type	True	79.4356	454	1695	95	below_threshold
Sporomusa termitida	strain=DSM 4440	GCA_007641255.1	2377	2377	type	True	79.2429	563	1695	95	below_threshold
Sporomusa sphaeroides	strain=DSM 2875	GCA_001941975.1	47679	47679	type	True	78.9969	435	1695	95	below_threshold
Sporomusa ovata	strain=DSM 2662	GCA_000445445.1	2378	2378	type	True	78.9182	444	1695	95	below_threshold
Sporomusa ovata	strain=DSM 2662	GCA_000423685.1	2378	2378	type	True	78.8981	440	1695	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:27,888] [INFO] DFAST Taxonomy check result was written to GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:27,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:27,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:27,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33494787-caf9-486d-86dd-4c8305dbe12e/dqc_reference/checkm_data
[2024-01-24 13:22:27,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:27,938] [INFO] Task started: CheckM
[2024-01-24 13:22:27,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/checkm_input GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:09,848] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:09,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:09,864] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:09,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:09,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:09,865] [INFO] Task started: Blastn
[2024-01-24 13:23:09,865] [INFO] Running command: blastn -query GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg33494787-caf9-486d-86dd-4c8305dbe12e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:10,678] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:10,681] [INFO] Selected 20 target genomes.
[2024-01-24 13:23:10,681] [INFO] Target genome list was writen to GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:10,748] [INFO] Task started: fastANI
[2024-01-24 13:23:10,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e80f21c-43e8-4a0c-8e17-07213f8c9b05/GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna.gz --refList GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:23,070] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:23,084] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:23,084] [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_900176355.1	s__Sporomusa malonica	100.0	1690	1695	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002257705.1	s__Sporomusa silvacetica	79.504	526	1695	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007641255.1	s__Sporomusa termitida	79.2458	565	1695	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830295.1	s__Sporomusa sp007830295	79.2317	480	1695	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941975.1	s__Sporomusa sphaeroides	78.9768	435	1695	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	98.27	97.38	0.92	0.86	4	-
GCF_000445445.1	s__Sporomusa ovata	78.8931	449	1695	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.96	99.93	1.00	0.99	3	-
GCA_017889675.1	s__Sporomusa sp017889675	78.5971	272	1695	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298735.1	s__CYSP01 sp001298735	76.9697	58	1695	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__CYSP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:23,086] [INFO] GTDB search result was written to GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:23,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:23,090] [INFO] DFAST_QC result json was written to GCF_900176355.1_IMG-taxon_2622736529_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:23,090] [INFO] DFAST_QC completed!
[2024-01-24 13:23:23,090] [INFO] Total running time: 0h1m21s