[2023-06-29 20:34:11,150] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:34:11,158] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:34:11,159] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dfec2df-91a4-461e-b4fa-dfdc2edb4087/dqc_reference
[2023-06-29 20:34:12,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:34:12,650] [INFO] Task started: Prodigal
[2023-06-29 20:34:12,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg60ca05dd-6686-46d8-a3e2-2323462c8488/GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:34:22,019] [INFO] Task succeeded: Prodigal
[2023-06-29 20:34:22,020] [INFO] Task started: HMMsearch
[2023-06-29 20:34:22,020] [INFO] Running command: hmmsearch --tblout GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dfec2df-91a4-461e-b4fa-dfdc2edb4087/dqc_reference/reference_markers.hmm GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:34:22,280] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:34:22,281] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg60ca05dd-6686-46d8-a3e2-2323462c8488/GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 20:34:22,313] [INFO] Query marker FASTA was written to GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 20:34:22,314] [INFO] Task started: Blastn
[2023-06-29 20:34:22,314] [INFO] Running command: blastn -query GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dfec2df-91a4-461e-b4fa-dfdc2edb4087/dqc_reference/reference_markers.fasta -out GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:34:22,833] [INFO] Task succeeded: Blastn
[2023-06-29 20:34:22,837] [INFO] Selected 12 target genomes.
[2023-06-29 20:34:22,838] [INFO] Target genome list was writen to GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 20:34:22,839] [INFO] Task started: fastANI
[2023-06-29 20:34:22,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg60ca05dd-6686-46d8-a3e2-2323462c8488/GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:34:34,201] [INFO] Task succeeded: fastANI
[2023-06-29 20:34:34,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dfec2df-91a4-461e-b4fa-dfdc2edb4087/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:34:34,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dfec2df-91a4-461e-b4fa-dfdc2edb4087/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:34:34,222] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:34:34,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:34:34,222] [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
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.3908	160	1027	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	77.3612	144	1027	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	77.3011	205	1027	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	77.1995	117	1027	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	77.0249	136	1027	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	76.9616	183	1027	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	76.6419	58	1027	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	76.5203	132	1027	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.2321	70	1027	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.1809	87	1027	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.1809	87	1027	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:34:34,225] [INFO] DFAST Taxonomy check result was written to GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 20:34:34,226] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:34:34,226] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:34:34,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dfec2df-91a4-461e-b4fa-dfdc2edb4087/dqc_reference/checkm_data
[2023-06-29 20:34:34,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:34:34,266] [INFO] Task started: CheckM
[2023-06-29 20:34:34,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 20:35:05,433] [INFO] Task succeeded: CheckM
[2023-06-29 20:35:05,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:35:05,456] [INFO] ===== Completeness check finished =====
[2023-06-29 20:35:05,456] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:35:05,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 20:35:05,457] [INFO] Task started: Blastn
[2023-06-29 20:35:05,457] [INFO] Running command: blastn -query GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dfec2df-91a4-461e-b4fa-dfdc2edb4087/dqc_reference/reference_markers_gtdb.fasta -out GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:35:05,998] [INFO] Task succeeded: Blastn
[2023-06-29 20:35:06,003] [INFO] Selected 13 target genomes.
[2023-06-29 20:35:06,004] [INFO] Target genome list was writen to GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:35:06,007] [INFO] Task started: fastANI
[2023-06-29 20:35:06,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg60ca05dd-6686-46d8-a3e2-2323462c8488/GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:35:17,002] [INFO] Task succeeded: fastANI
[2023-06-29 20:35:17,019] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:35:17,020] [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_013410115.1	s__Edaphobacter lichenicola_A	77.3563	166	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	98.03	98.03	0.94	0.94	2	-
GCF_000745965.1	s__Edaphobacter aggregans	77.3011	205	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003945235.1	s__Edaphobacter aggregans_A	77.2718	159	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217555.1	s__Edaphobacter modestus	77.1995	117	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873705.1	s__CAIQPK01 sp903873705	77.0815	119	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIQPK01	95.0	99.92	99.91	0.95	0.94	3	-
GCA_000421065.1	s__Edaphobacter sp000421065	77.0792	155	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201335.1	s__Edaphobacter lichenicola_E	77.0193	151	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188085.1	s__Granulicella_C rosea	76.9756	183	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268775.1	s__Edaphobacter sp018268775	76.8687	152	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132145.1	s__Palsa-288 sp003132145	76.7833	119	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	99.75	99.72	0.90	0.88	3	-
GCF_014203225.1	s__Granulicella_A mallensis_A	76.7581	139	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970395.1	s__UBA5172 sp903970395	76.6601	109	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022565.1	s__Acidobacterium capsulatum	76.2321	70	1027	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-29 20:35:17,024] [INFO] GTDB search result was written to GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 20:35:17,024] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:35:17,028] [INFO] DFAST_QC result json was written to GCA_937873265.1_SRR13685148_bin.7_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 20:35:17,029] [INFO] DFAST_QC completed!
[2023-06-29 20:35:17,029] [INFO] Total running time: 0h1m6s