[2023-06-08 12:31:47,603] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:31:47,610] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:31:47,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg84d3be62-ff07-490d-8bb7-f5d9df8017d1/dqc_reference
[2023-06-08 12:31:48,867] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:31:48,868] [INFO] Task started: Prodigal
[2023-06-08 12:31:48,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg806e11ea-cf10-49df-8046-b8497b1cddde/GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:31:53,048] [INFO] Task succeeded: Prodigal
[2023-06-08 12:31:53,049] [INFO] Task started: HMMsearch
[2023-06-08 12:31:53,049] [INFO] Running command: hmmsearch --tblout GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84d3be62-ff07-490d-8bb7-f5d9df8017d1/dqc_reference/reference_markers.hmm GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:31:53,275] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:31:53,276] [INFO] Found 6/6 markers.
[2023-06-08 12:31:53,298] [INFO] Query marker FASTA was written to GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:31:53,299] [INFO] Task started: Blastn
[2023-06-08 12:31:53,299] [INFO] Running command: blastn -query GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d3be62-ff07-490d-8bb7-f5d9df8017d1/dqc_reference/reference_markers.fasta -out GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:31:53,976] [INFO] Task succeeded: Blastn
[2023-06-08 12:31:53,987] [INFO] Selected 10 target genomes.
[2023-06-08 12:31:53,988] [INFO] Target genome list was writen to GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:31:53,989] [INFO] Task started: fastANI
[2023-06-08 12:31:53,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg806e11ea-cf10-49df-8046-b8497b1cddde/GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:32:00,664] [INFO] Task succeeded: fastANI
[2023-06-08 12:32:00,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84d3be62-ff07-490d-8bb7-f5d9df8017d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:32:00,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84d3be62-ff07-490d-8bb7-f5d9df8017d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:32:00,680] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 12:32:00,681] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 12:32:00,681] [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
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	95.8935	372	374	95	conclusive
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	80.0969	222	374	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	78.931	184	374	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	78.3761	113	374	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	78.3138	134	374	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.5819	86	374	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	77.3562	82	374	95	below_threshold
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	76.8805	77	374	95	below_threshold
Desulfomicrobium apsheronum	strain=DSM 5918	GCA_900114115.1	52560	52560	type	True	75.913	52	374	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:32:00,684] [INFO] DFAST Taxonomy check result was written to GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:32:00,685] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:32:00,686] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:32:00,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84d3be62-ff07-490d-8bb7-f5d9df8017d1/dqc_reference/checkm_data
[2023-06-08 12:32:00,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:32:00,707] [INFO] Task started: CheckM
[2023-06-08 12:32:00,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:32:19,198] [INFO] Task succeeded: CheckM
[2023-06-08 12:32:19,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:32:19,219] [INFO] ===== Completeness check finished =====
[2023-06-08 12:32:19,219] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:32:19,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:32:19,220] [INFO] Task started: Blastn
[2023-06-08 12:32:19,220] [INFO] Running command: blastn -query GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d3be62-ff07-490d-8bb7-f5d9df8017d1/dqc_reference/reference_markers_gtdb.fasta -out GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:32:20,262] [INFO] Task succeeded: Blastn
[2023-06-08 12:32:20,267] [INFO] Selected 9 target genomes.
[2023-06-08 12:32:20,267] [INFO] Target genome list was writen to GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:32:20,270] [INFO] Task started: fastANI
[2023-06-08 12:32:20,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg806e11ea-cf10-49df-8046-b8497b1cddde/GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:32:24,627] [INFO] Task succeeded: fastANI
[2023-06-08 12:32:24,640] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-08 12:32:24,640] [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_012843875.1	s__Desulfovibrio sp900556755	99.3611	368	374	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	98.27	96.78	0.88	0.81	10	inconclusive
GCF_000156375.1	s__Desulfovibrio piger	95.8935	372	374	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	99.18	98.09	0.98	0.96	5	inconclusive
GCF_900116045.1	s__Desulfovibrio piger_A	94.4348	360	374	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.11	98.95	0.94	0.93	3	-
GCA_019118745.1	s__Desulfovibrio gallistercoris	80.9721	224	374	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696265.1	s__Desulfovibrio porci	80.0969	222	374	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.64	99.64	0.91	0.91	2	-
GCA_905215675.1	s__Desulfovibrio sp905215675	80.0744	176	374	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118345.1	s__Desulfovibrio intestinavium	79.9711	224	374	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062205.1	s__Desulfovibrio desulfuricans_D	79.4533	183	374	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801255.1	s__Desulfovibrio desulfuricans_C	79.0349	172	374	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:32:24,642] [INFO] GTDB search result was written to GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:32:24,643] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:32:24,646] [INFO] DFAST_QC result json was written to GCA_945492575.1_SRR7188235_bin.55_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:32:24,646] [INFO] DFAST_QC completed!
[2023-06-08 12:32:24,646] [INFO] Total running time: 0h0m37s