[2023-06-05 18:35:07,258] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:35:07,266] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:35:07,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bf83037-7cba-4f72-98f2-2b4fdd9f1b98/dqc_reference
[2023-06-05 18:35:09,033] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:35:09,033] [INFO] Task started: Prodigal
[2023-06-05 18:35:09,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f392c24-3d14-421e-9e91-dfe60005ed71/GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna.gz | prodigal -d GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/cds.fna -a GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:35:16,407] [INFO] Task succeeded: Prodigal
[2023-06-05 18:35:16,408] [INFO] Task started: HMMsearch
[2023-06-05 18:35:16,408] [INFO] Running command: hmmsearch --tblout GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bf83037-7cba-4f72-98f2-2b4fdd9f1b98/dqc_reference/reference_markers.hmm GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:35:16,633] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:35:16,634] [INFO] Found 6/6 markers.
[2023-06-05 18:35:16,657] [INFO] Query marker FASTA was written to GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/markers.fasta
[2023-06-05 18:35:16,657] [INFO] Task started: Blastn
[2023-06-05 18:35:16,658] [INFO] Running command: blastn -query GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bf83037-7cba-4f72-98f2-2b4fdd9f1b98/dqc_reference/reference_markers.fasta -out GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:35:17,371] [INFO] Task succeeded: Blastn
[2023-06-05 18:35:17,375] [INFO] Selected 8 target genomes.
[2023-06-05 18:35:17,376] [INFO] Target genome list was writen to GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/target_genomes.txt
[2023-06-05 18:35:17,380] [INFO] Task started: fastANI
[2023-06-05 18:35:17,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f392c24-3d14-421e-9e91-dfe60005ed71/GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna.gz --refList GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/target_genomes.txt --output GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:35:22,752] [INFO] Task succeeded: fastANI
[2023-06-05 18:35:22,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bf83037-7cba-4f72-98f2-2b4fdd9f1b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:35:22,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bf83037-7cba-4f72-98f2-2b4fdd9f1b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:35:22,761] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:35:22,761] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:35:22,762] [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	93.9253	688	752	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	80.2577	399	752	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	79.2522	321	752	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	78.6229	196	752	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	78.4493	208	752	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	78.2553	218	752	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	78.1532	249	752	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.7162	163	752	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:35:22,764] [INFO] DFAST Taxonomy check result was written to GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/tc_result.tsv
[2023-06-05 18:35:22,764] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:35:22,764] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:35:22,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bf83037-7cba-4f72-98f2-2b4fdd9f1b98/dqc_reference/checkm_data
[2023-06-05 18:35:22,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:35:22,794] [INFO] Task started: CheckM
[2023-06-05 18:35:22,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/checkm_input GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/checkm_result
[2023-06-05 18:35:48,339] [INFO] Task succeeded: CheckM
[2023-06-05 18:35:48,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:35:48,444] [INFO] ===== Completeness check finished =====
[2023-06-05 18:35:48,444] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:35:48,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/markers.fasta)
[2023-06-05 18:35:48,445] [INFO] Task started: Blastn
[2023-06-05 18:35:48,445] [INFO] Running command: blastn -query GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bf83037-7cba-4f72-98f2-2b4fdd9f1b98/dqc_reference/reference_markers_gtdb.fasta -out GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:35:49,505] [INFO] Task succeeded: Blastn
[2023-06-05 18:35:49,509] [INFO] Selected 11 target genomes.
[2023-06-05 18:35:49,509] [INFO] Target genome list was writen to GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:35:49,536] [INFO] Task started: fastANI
[2023-06-05 18:35:49,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f392c24-3d14-421e-9e91-dfe60005ed71/GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna.gz --refList GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/target_genomes_gtdb.txt --output GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:35:57,665] [INFO] Task succeeded: fastANI
[2023-06-05 18:35:57,676] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:35:57,676] [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_900116045.1	s__Desulfovibrio piger_A	99.2654	724	752	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.11	98.95	0.94	0.93	3	conclusive
GCF_000156375.1	s__Desulfovibrio piger	93.9253	688	752	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	99.18	98.09	0.98	0.96	5	-
GCF_012843875.1	s__Desulfovibrio sp900556755	93.8274	643	752	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	98.27	96.78	0.88	0.81	10	-
GCA_019118745.1	s__Desulfovibrio gallistercoris	80.8871	405	752	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	80.3472	377	752	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	80.2553	400	752	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_019114565.1	s__Desulfovibrio intestinigallinarum	79.9595	302	752	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_001553605.1	s__Desulfovibrio fairfieldensis	79.8654	414	752	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	97.09	95.23	0.86	0.83	6	-
GCA_905215675.1	s__Desulfovibrio sp905215675	79.7634	278	752	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	79.5396	340	752	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_910575755.1	s__Desulfovibrio sp910575755	79.4707	337	752	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:35:57,678] [INFO] GTDB search result was written to GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/result_gtdb.tsv
[2023-06-05 18:35:57,679] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:35:57,682] [INFO] DFAST_QC result json was written to GCA_902406005.1_UHGG_MGYG-HGUT-04253_genomic.fna/dqc_result.json
[2023-06-05 18:35:57,682] [INFO] DFAST_QC completed!
[2023-06-05 18:35:57,682] [INFO] Total running time: 0h0m50s