[2023-06-29 00:38:16,166] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:38:16,172] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:38:16,172] [INFO] DQC Reference Directory: /var/lib/cwl/stgeda20b03-6ad9-42d5-b992-cd2bf05eb835/dqc_reference
[2023-06-29 00:38:18,732] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:38:18,734] [INFO] Task started: Prodigal
[2023-06-29 00:38:18,734] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1595571-3b11-45a5-a70d-0839434285c6/GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:38:24,196] [INFO] Task succeeded: Prodigal
[2023-06-29 00:38:24,196] [INFO] Task started: HMMsearch
[2023-06-29 00:38:24,196] [INFO] Running command: hmmsearch --tblout GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeda20b03-6ad9-42d5-b992-cd2bf05eb835/dqc_reference/reference_markers.hmm GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:38:24,435] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:38:24,436] [INFO] Found 6/6 markers.
[2023-06-29 00:38:24,462] [INFO] Query marker FASTA was written to GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 00:38:24,463] [INFO] Task started: Blastn
[2023-06-29 00:38:24,463] [INFO] Running command: blastn -query GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeda20b03-6ad9-42d5-b992-cd2bf05eb835/dqc_reference/reference_markers.fasta -out GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:25,145] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:25,150] [INFO] Selected 8 target genomes.
[2023-06-29 00:38:25,150] [INFO] Target genome list was writen to GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 00:38:25,152] [INFO] Task started: fastANI
[2023-06-29 00:38:25,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1595571-3b11-45a5-a70d-0839434285c6/GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:38:29,571] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:29,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeda20b03-6ad9-42d5-b992-cd2bf05eb835/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:38:29,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeda20b03-6ad9-42d5-b992-cd2bf05eb835/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:38:29,587] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:38:29,588] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:38:29,588] [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	79.2274	281	593	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	78.9626	262	593	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	77.752	194	593	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	77.3045	122	593	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.2827	107	593	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.2491	134	593	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	76.3	64	593	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	75.6693	79	593	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:38:29,591] [INFO] DFAST Taxonomy check result was written to GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 00:38:29,591] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:38:29,592] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:38:29,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeda20b03-6ad9-42d5-b992-cd2bf05eb835/dqc_reference/checkm_data
[2023-06-29 00:38:29,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:38:29,619] [INFO] Task started: CheckM
[2023-06-29 00:38:29,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 00:38:51,442] [INFO] Task succeeded: CheckM
[2023-06-29 00:38:51,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:38:51,467] [INFO] ===== Completeness check finished =====
[2023-06-29 00:38:51,467] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:38:51,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 00:38:51,468] [INFO] Task started: Blastn
[2023-06-29 00:38:51,468] [INFO] Running command: blastn -query GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeda20b03-6ad9-42d5-b992-cd2bf05eb835/dqc_reference/reference_markers_gtdb.fasta -out GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:52,576] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:52,582] [INFO] Selected 12 target genomes.
[2023-06-29 00:38:52,582] [INFO] Target genome list was writen to GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:38:52,592] [INFO] Task started: fastANI
[2023-06-29 00:38:52,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1595571-3b11-45a5-a70d-0839434285c6/GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:39:00,741] [INFO] Task succeeded: fastANI
[2023-06-29 00:39:00,752] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:39:00,753] [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
GCA_905215675.1	s__Desulfovibrio sp905215675	98.3114	451	593	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019114565.1	s__Desulfovibrio intestinigallinarum	86.8901	470	593	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_900116045.1	s__Desulfovibrio piger_A	79.4097	292	593	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.11	98.95	0.94	0.93	3	-
GCF_012843875.1	s__Desulfovibrio sp900556755	79.3576	265	593	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	98.27	96.78	0.88	0.81	10	-
GCF_000156375.1	s__Desulfovibrio piger	79.2101	282	593	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	99.18	98.09	0.98	0.96	5	-
GCA_019118345.1	s__Desulfovibrio intestinavium	79.2001	273	593	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	78.9832	293	593	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	78.7014	249	593	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_015062205.1	s__Desulfovibrio desulfuricans_D	78.5919	226	593	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_011039085.1	s__Desulfovibrio sp011039085	77.7529	218	593	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.72	96.72	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-29 00:39:00,755] [INFO] GTDB search result was written to GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 00:39:00,756] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:39:00,759] [INFO] DFAST_QC result json was written to GCA_948437405.1_SRR17622769_bin.44_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 00:39:00,759] [INFO] DFAST_QC completed!
[2023-06-29 00:39:00,759] [INFO] Total running time: 0h0m45s