[2023-06-28 19:48:19,150] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:19,154] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:19,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c4a29f3-39a8-4db3-a83e-e12a29164886/dqc_reference
[2023-06-28 19:48:21,577] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:21,578] [INFO] Task started: Prodigal
[2023-06-28 19:48:21,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg9936f61b-d492-4e18-ac94-c89034982772/GCA_944324065.1_BRZ_B_bin14_genomic.fna.gz | prodigal -d GCA_944324065.1_BRZ_B_bin14_genomic.fna/cds.fna -a GCA_944324065.1_BRZ_B_bin14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:29,802] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:29,803] [INFO] Task started: HMMsearch
[2023-06-28 19:48:29,803] [INFO] Running command: hmmsearch --tblout GCA_944324065.1_BRZ_B_bin14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c4a29f3-39a8-4db3-a83e-e12a29164886/dqc_reference/reference_markers.hmm GCA_944324065.1_BRZ_B_bin14_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:30,006] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:30,008] [INFO] Found 6/6 markers.
[2023-06-28 19:48:30,032] [INFO] Query marker FASTA was written to GCA_944324065.1_BRZ_B_bin14_genomic.fna/markers.fasta
[2023-06-28 19:48:30,032] [INFO] Task started: Blastn
[2023-06-28 19:48:30,033] [INFO] Running command: blastn -query GCA_944324065.1_BRZ_B_bin14_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c4a29f3-39a8-4db3-a83e-e12a29164886/dqc_reference/reference_markers.fasta -out GCA_944324065.1_BRZ_B_bin14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:30,683] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:30,688] [INFO] Selected 10 target genomes.
[2023-06-28 19:48:30,689] [INFO] Target genome list was writen to GCA_944324065.1_BRZ_B_bin14_genomic.fna/target_genomes.txt
[2023-06-28 19:48:30,690] [INFO] Task started: fastANI
[2023-06-28 19:48:30,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg9936f61b-d492-4e18-ac94-c89034982772/GCA_944324065.1_BRZ_B_bin14_genomic.fna.gz --refList GCA_944324065.1_BRZ_B_bin14_genomic.fna/target_genomes.txt --output GCA_944324065.1_BRZ_B_bin14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:37,782] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:37,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c4a29f3-39a8-4db3-a83e-e12a29164886/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:37,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c4a29f3-39a8-4db3-a83e-e12a29164886/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:37,792] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 19:48:37,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 19:48:37,793] [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	95.3637	770	873	95	conclusive
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	79.973	412	873	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	78.9528	333	873	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	78.3971	235	873	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	78.3006	209	873	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	77.9093	168	873	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.7429	181	873	95	below_threshold
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	77.2873	135	873	95	below_threshold
Desulfomicrobium apsheronum	strain=DSM 5918	GCA_900114115.1	52560	52560	type	True	76.7707	97	873	95	below_threshold
Desulfonatronum lacustre	strain=DSM 10312	GCA_000519265.1	66849	66849	type	True	76.2158	74	873	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:48:37,794] [INFO] DFAST Taxonomy check result was written to GCA_944324065.1_BRZ_B_bin14_genomic.fna/tc_result.tsv
[2023-06-28 19:48:37,795] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:37,795] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:37,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c4a29f3-39a8-4db3-a83e-e12a29164886/dqc_reference/checkm_data
[2023-06-28 19:48:37,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:37,825] [INFO] Task started: CheckM
[2023-06-28 19:48:37,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944324065.1_BRZ_B_bin14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944324065.1_BRZ_B_bin14_genomic.fna/checkm_input GCA_944324065.1_BRZ_B_bin14_genomic.fna/checkm_result
[2023-06-28 19:49:06,445] [INFO] Task succeeded: CheckM
[2023-06-28 19:49:06,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:49:06,463] [INFO] ===== Completeness check finished =====
[2023-06-28 19:49:06,463] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:49:06,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944324065.1_BRZ_B_bin14_genomic.fna/markers.fasta)
[2023-06-28 19:49:06,463] [INFO] Task started: Blastn
[2023-06-28 19:49:06,464] [INFO] Running command: blastn -query GCA_944324065.1_BRZ_B_bin14_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c4a29f3-39a8-4db3-a83e-e12a29164886/dqc_reference/reference_markers_gtdb.fasta -out GCA_944324065.1_BRZ_B_bin14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:07,480] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:07,484] [INFO] Selected 11 target genomes.
[2023-06-28 19:49:07,484] [INFO] Target genome list was writen to GCA_944324065.1_BRZ_B_bin14_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:49:07,486] [INFO] Task started: fastANI
[2023-06-28 19:49:07,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg9936f61b-d492-4e18-ac94-c89034982772/GCA_944324065.1_BRZ_B_bin14_genomic.fna.gz --refList GCA_944324065.1_BRZ_B_bin14_genomic.fna/target_genomes_gtdb.txt --output GCA_944324065.1_BRZ_B_bin14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:49:14,406] [INFO] Task succeeded: fastANI
[2023-06-28 19:49:14,416] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 19:49:14,416] [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	98.3355	735	873	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	95.3637	770	873	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	93.7779	740	873	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	81.1351	425	873	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	80.2129	407	873	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_019114565.1	s__Desulfovibrio intestinigallinarum	79.9522	340	873	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_905215675.1	s__Desulfovibrio sp905215675	79.9501	280	873	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	79.9475	414	873	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_015062205.1	s__Desulfovibrio desulfuricans_D	79.205	362	873	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	79.0608	308	873	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_000403945.1	s__Desulfovibrio sp000403945	78.9028	279	873	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:49:14,418] [INFO] GTDB search result was written to GCA_944324065.1_BRZ_B_bin14_genomic.fna/result_gtdb.tsv
[2023-06-28 19:49:14,419] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:49:14,422] [INFO] DFAST_QC result json was written to GCA_944324065.1_BRZ_B_bin14_genomic.fna/dqc_result.json
[2023-06-28 19:49:14,422] [INFO] DFAST_QC completed!
[2023-06-28 19:49:14,422] [INFO] Total running time: 0h0m55s