[2024-01-24 12:40:03,758] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:03,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:03,761] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6e99689-af76-452e-9cdf-d490c7f6157f/dqc_reference
[2024-01-24 12:40:04,965] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:04,966] [INFO] Task started: Prodigal
[2024-01-24 12:40:04,966] [INFO] Running command: gunzip -c /var/lib/cwl/stg9299b09a-7900-4b4a-9c7e-c60bc111d29a/GCF_000421285.1_ASM42128v1_genomic.fna.gz | prodigal -d GCF_000421285.1_ASM42128v1_genomic.fna/cds.fna -a GCF_000421285.1_ASM42128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:22,376] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:22,377] [INFO] Task started: HMMsearch
[2024-01-24 12:40:22,377] [INFO] Running command: hmmsearch --tblout GCF_000421285.1_ASM42128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6e99689-af76-452e-9cdf-d490c7f6157f/dqc_reference/reference_markers.hmm GCF_000421285.1_ASM42128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:22,685] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:22,686] [INFO] Found 6/6 markers.
[2024-01-24 12:40:22,731] [INFO] Query marker FASTA was written to GCF_000421285.1_ASM42128v1_genomic.fna/markers.fasta
[2024-01-24 12:40:22,731] [INFO] Task started: Blastn
[2024-01-24 12:40:22,731] [INFO] Running command: blastn -query GCF_000421285.1_ASM42128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6e99689-af76-452e-9cdf-d490c7f6157f/dqc_reference/reference_markers.fasta -out GCF_000421285.1_ASM42128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:23,315] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:23,320] [INFO] Selected 18 target genomes.
[2024-01-24 12:40:23,321] [INFO] Target genome list was writen to GCF_000421285.1_ASM42128v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:23,330] [INFO] Task started: fastANI
[2024-01-24 12:40:23,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg9299b09a-7900-4b4a-9c7e-c60bc111d29a/GCF_000421285.1_ASM42128v1_genomic.fna.gz --refList GCF_000421285.1_ASM42128v1_genomic.fna/target_genomes.txt --output GCF_000421285.1_ASM42128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:39,007] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:39,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6e99689-af76-452e-9cdf-d490c7f6157f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:39,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6e99689-af76-452e-9cdf-d490c7f6157f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:39,023] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:39,023] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:40:39,024] [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
Desulfotignum balticum	strain=DSM 7044	GCA_000421285.1	115781	115781	type	True	100.0	1703	1704	95	inconclusive
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	96.8503	1294	1704	95	inconclusive
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	77.5514	360	1704	95	below_threshold
Desulfobacter latus	strain=AcRS2	GCA_013389365.1	2292	2292	type	True	77.3923	172	1704	95	below_threshold
Desulfobacter postgatei	strain=2ac9	GCA_000233695.3	2293	2293	type	True	77.3343	150	1704	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	77.1436	208	1704	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	76.1931	106	1704	95	below_threshold
Desulfosudis oleivorans	strain=Hxd3	GCA_000018405.1	181663	181663	type	True	76.1675	101	1704	95	below_threshold
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	75.7019	85	1704	95	below_threshold
Desulfoluna spongiiphila	strain=AA1	GCA_900101345.1	419481	419481	type	True	75.683	69	1704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:39,032] [INFO] DFAST Taxonomy check result was written to GCF_000421285.1_ASM42128v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:39,033] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:39,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:39,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6e99689-af76-452e-9cdf-d490c7f6157f/dqc_reference/checkm_data
[2024-01-24 12:40:39,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:39,083] [INFO] Task started: CheckM
[2024-01-24 12:40:39,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421285.1_ASM42128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421285.1_ASM42128v1_genomic.fna/checkm_input GCF_000421285.1_ASM42128v1_genomic.fna/checkm_result
[2024-01-24 12:41:31,311] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:31,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:31,330] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:31,331] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:31,331] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421285.1_ASM42128v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:31,332] [INFO] Task started: Blastn
[2024-01-24 12:41:31,332] [INFO] Running command: blastn -query GCF_000421285.1_ASM42128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6e99689-af76-452e-9cdf-d490c7f6157f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421285.1_ASM42128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:32,097] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:32,101] [INFO] Selected 7 target genomes.
[2024-01-24 12:41:32,101] [INFO] Target genome list was writen to GCF_000421285.1_ASM42128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:32,124] [INFO] Task started: fastANI
[2024-01-24 12:41:32,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg9299b09a-7900-4b4a-9c7e-c60bc111d29a/GCF_000421285.1_ASM42128v1_genomic.fna.gz --refList GCF_000421285.1_ASM42128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421285.1_ASM42128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:39,229] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:39,243] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:39,243] [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_000421285.1	s__Desulfotignum balticum	100.0	1703	1704	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	conclusive
GCF_000350545.1	s__Desulfotignum phosphitoxidans	96.8536	1295	1704	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	-
GCA_018399285.1	s__Desulfotignum sp018399285	94.3703	913	1704	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389555.1	s__Desulfotignum sp011389555	87.7233	813	1704	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389835.1	s__Desulfotignum sp011389835	85.0842	711	1704	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390335.1	s__Desulfotignum sp011390335	81.8031	802	1704	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390695.1	s__Desulfotignum sp011390695	81.6046	358	1704	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:39,245] [INFO] GTDB search result was written to GCF_000421285.1_ASM42128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:39,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:39,248] [INFO] DFAST_QC result json was written to GCF_000421285.1_ASM42128v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:39,248] [INFO] DFAST_QC completed!
[2024-01-24 12:41:39,248] [INFO] Total running time: 0h1m35s