[2023-06-28 20:27:12,857] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:27:12,861] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:27:12,861] [INFO] DQC Reference Directory: /var/lib/cwl/stg54f7141e-f93f-4d39-a220-3d6b18826e19/dqc_reference
[2023-06-28 20:27:14,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:27:14,472] [INFO] Task started: Prodigal
[2023-06-28 20:27:14,472] [INFO] Running command: gunzip -c /var/lib/cwl/stgfaa90c5a-9cde-4f97-b032-373ed3953b9e/GCA_944324535.1_BRZ_ED_bin25_genomic.fna.gz | prodigal -d GCA_944324535.1_BRZ_ED_bin25_genomic.fna/cds.fna -a GCA_944324535.1_BRZ_ED_bin25_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:27:23,677] [INFO] Task succeeded: Prodigal
[2023-06-28 20:27:23,677] [INFO] Task started: HMMsearch
[2023-06-28 20:27:23,677] [INFO] Running command: hmmsearch --tblout GCA_944324535.1_BRZ_ED_bin25_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54f7141e-f93f-4d39-a220-3d6b18826e19/dqc_reference/reference_markers.hmm GCA_944324535.1_BRZ_ED_bin25_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:27:23,939] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:27:23,940] [INFO] Found 6/6 markers.
[2023-06-28 20:27:23,973] [INFO] Query marker FASTA was written to GCA_944324535.1_BRZ_ED_bin25_genomic.fna/markers.fasta
[2023-06-28 20:27:23,973] [INFO] Task started: Blastn
[2023-06-28 20:27:23,974] [INFO] Running command: blastn -query GCA_944324535.1_BRZ_ED_bin25_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f7141e-f93f-4d39-a220-3d6b18826e19/dqc_reference/reference_markers.fasta -out GCA_944324535.1_BRZ_ED_bin25_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:27:24,623] [INFO] Task succeeded: Blastn
[2023-06-28 20:27:24,627] [INFO] Selected 22 target genomes.
[2023-06-28 20:27:24,628] [INFO] Target genome list was writen to GCA_944324535.1_BRZ_ED_bin25_genomic.fna/target_genomes.txt
[2023-06-28 20:27:24,632] [INFO] Task started: fastANI
[2023-06-28 20:27:24,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaa90c5a-9cde-4f97-b032-373ed3953b9e/GCA_944324535.1_BRZ_ED_bin25_genomic.fna.gz --refList GCA_944324535.1_BRZ_ED_bin25_genomic.fna/target_genomes.txt --output GCA_944324535.1_BRZ_ED_bin25_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:27:41,570] [INFO] Task succeeded: fastANI
[2023-06-28 20:27:41,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54f7141e-f93f-4d39-a220-3d6b18826e19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:27:41,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54f7141e-f93f-4d39-a220-3d6b18826e19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:27:41,584] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:27:41,584] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:27:41,584] [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	77.774	163	890	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	76.8396	76	890	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	76.7377	138	890	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	76.5705	108	890	95	below_threshold
Mailhella massiliensis	strain=Marseille-P3199	GCA_900155525.1	1903261	1903261	type	True	76.2021	79	890	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:27:41,586] [INFO] DFAST Taxonomy check result was written to GCA_944324535.1_BRZ_ED_bin25_genomic.fna/tc_result.tsv
[2023-06-28 20:27:41,587] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:27:41,587] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:27:41,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54f7141e-f93f-4d39-a220-3d6b18826e19/dqc_reference/checkm_data
[2023-06-28 20:27:41,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:27:41,633] [INFO] Task started: CheckM
[2023-06-28 20:27:41,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944324535.1_BRZ_ED_bin25_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944324535.1_BRZ_ED_bin25_genomic.fna/checkm_input GCA_944324535.1_BRZ_ED_bin25_genomic.fna/checkm_result
[2023-06-28 20:28:13,198] [INFO] Task succeeded: CheckM
[2023-06-28 20:28:13,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:28:13,225] [INFO] ===== Completeness check finished =====
[2023-06-28 20:28:13,226] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:28:13,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944324535.1_BRZ_ED_bin25_genomic.fna/markers.fasta)
[2023-06-28 20:28:13,226] [INFO] Task started: Blastn
[2023-06-28 20:28:13,227] [INFO] Running command: blastn -query GCA_944324535.1_BRZ_ED_bin25_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f7141e-f93f-4d39-a220-3d6b18826e19/dqc_reference/reference_markers_gtdb.fasta -out GCA_944324535.1_BRZ_ED_bin25_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:28:14,016] [INFO] Task succeeded: Blastn
[2023-06-28 20:28:14,021] [INFO] Selected 21 target genomes.
[2023-06-28 20:28:14,021] [INFO] Target genome list was writen to GCA_944324535.1_BRZ_ED_bin25_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:28:14,035] [INFO] Task started: fastANI
[2023-06-28 20:28:14,035] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaa90c5a-9cde-4f97-b032-373ed3953b9e/GCA_944324535.1_BRZ_ED_bin25_genomic.fna.gz --refList GCA_944324535.1_BRZ_ED_bin25_genomic.fna/target_genomes_gtdb.txt --output GCA_944324535.1_BRZ_ED_bin25_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:28:24,858] [INFO] Task succeeded: fastANI
[2023-06-28 20:28:24,876] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:28:24,877] [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_002159665.1	s__Desulfovibrio faecigallinarum	97.9361	804	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	98.21	97.37	0.93	0.87	4	conclusive
GCA_019113165.1	s__Desulfovibrio intestinipullorum	80.1647	429	890	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_002369295.1	s__Desulfovibrio sp002369295	78.3751	160	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.45	99.45	0.84	0.84	2	-
GCA_016284885.1	s__Desulfovibrio sp016284885	77.8784	189	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.92	95.09	0.88	0.83	3	-
GCA_900546145.1	s__Desulfovibrio sp900546145	77.5607	156	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.05	98.98	0.92	0.90	3	-
GCA_015062205.1	s__Desulfovibrio desulfuricans_D	77.0628	126	890	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_019118745.1	s__Desulfovibrio gallistercoris	77.04	133	890	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	76.9214	124	890	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_014804965.1	s__Desulfovibrio sp014804965	76.9028	112	890	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_000420465.1	s__Desulfovibrio desulfuricans	76.8347	110	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.33	95.61	0.91	0.89	6	-
GCF_011682075.1	s__Cupidesulfovibrio liaohensis	76.7927	69	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015731765.1	s__Cupidesulfovibrio oxamicus	76.7884	77	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004309735.1	s__Desulfovibrio legallii	76.5705	108	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.59	99.44	0.93	0.93	5	-
GCF_900102485.1	s__Desulfovibrio legallii_A	76.5054	127	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.86	99.86	0.97	0.97	2	-
GCF_011039085.1	s__Desulfovibrio sp011039085	76.4187	92	890	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.72	96.72	0.85	0.85	2	-
GCA_017396005.1	s__Desulfovibrio sp017396005	76.2364	52	890	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 20:28:24,879] [INFO] GTDB search result was written to GCA_944324535.1_BRZ_ED_bin25_genomic.fna/result_gtdb.tsv
[2023-06-28 20:28:24,879] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:28:24,883] [INFO] DFAST_QC result json was written to GCA_944324535.1_BRZ_ED_bin25_genomic.fna/dqc_result.json
[2023-06-28 20:28:24,883] [INFO] DFAST_QC completed!
[2023-06-28 20:28:24,883] [INFO] Total running time: 0h1m12s