[2023-06-29 12:58:40,618] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:58:40,620] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:58:40,620] [INFO] DQC Reference Directory: /var/lib/cwl/stgec70c3ba-f2fe-415f-b298-18871d9cb402/dqc_reference
[2023-06-29 12:58:42,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:58:42,474] [INFO] Task started: Prodigal
[2023-06-29 12:58:42,474] [INFO] Running command: gunzip -c /var/lib/cwl/stg99a7c684-9534-464f-b323-0467060a5920/GCA_020072595.1_ASM2007259v1_genomic.fna.gz | prodigal -d GCA_020072595.1_ASM2007259v1_genomic.fna/cds.fna -a GCA_020072595.1_ASM2007259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:59:06,380] [INFO] Task succeeded: Prodigal
[2023-06-29 12:59:06,381] [INFO] Task started: HMMsearch
[2023-06-29 12:59:06,381] [INFO] Running command: hmmsearch --tblout GCA_020072595.1_ASM2007259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec70c3ba-f2fe-415f-b298-18871d9cb402/dqc_reference/reference_markers.hmm GCA_020072595.1_ASM2007259v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:59:06,700] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:59:06,701] [INFO] Found 6/6 markers.
[2023-06-29 12:59:06,754] [INFO] Query marker FASTA was written to GCA_020072595.1_ASM2007259v1_genomic.fna/markers.fasta
[2023-06-29 12:59:06,754] [INFO] Task started: Blastn
[2023-06-29 12:59:06,755] [INFO] Running command: blastn -query GCA_020072595.1_ASM2007259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec70c3ba-f2fe-415f-b298-18871d9cb402/dqc_reference/reference_markers.fasta -out GCA_020072595.1_ASM2007259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:59:07,420] [INFO] Task succeeded: Blastn
[2023-06-29 12:59:07,503] [INFO] Selected 22 target genomes.
[2023-06-29 12:59:07,504] [INFO] Target genome list was writen to GCA_020072595.1_ASM2007259v1_genomic.fna/target_genomes.txt
[2023-06-29 12:59:07,509] [INFO] Task started: fastANI
[2023-06-29 12:59:07,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg99a7c684-9534-464f-b323-0467060a5920/GCA_020072595.1_ASM2007259v1_genomic.fna.gz --refList GCA_020072595.1_ASM2007259v1_genomic.fna/target_genomes.txt --output GCA_020072595.1_ASM2007259v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:59:22,937] [INFO] Task succeeded: fastANI
[2023-06-29 12:59:22,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec70c3ba-f2fe-415f-b298-18871d9cb402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:59:22,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec70c3ba-f2fe-415f-b298-18871d9cb402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:59:22,960] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:59:22,960] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:59:22,960] [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
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.3482	84	2114	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.3456	81	2114	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	76.175	61	2114	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	76.1245	70	2114	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.0946	95	2114	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.089	97	2114	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.0218	87	2114	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	76.0201	72	2114	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	75.9956	87	2114	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	75.9708	59	2114	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	75.7443	71	2114	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	75.7082	72	2114	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:59:22,963] [INFO] DFAST Taxonomy check result was written to GCA_020072595.1_ASM2007259v1_genomic.fna/tc_result.tsv
[2023-06-29 12:59:22,963] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:59:22,963] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:59:22,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec70c3ba-f2fe-415f-b298-18871d9cb402/dqc_reference/checkm_data
[2023-06-29 12:59:22,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:59:23,030] [INFO] Task started: CheckM
[2023-06-29 12:59:23,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020072595.1_ASM2007259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020072595.1_ASM2007259v1_genomic.fna/checkm_input GCA_020072595.1_ASM2007259v1_genomic.fna/checkm_result
[2023-06-29 13:00:30,360] [INFO] Task succeeded: CheckM
[2023-06-29 13:00:30,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.42%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:00:30,389] [INFO] ===== Completeness check finished =====
[2023-06-29 13:00:30,389] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:00:30,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020072595.1_ASM2007259v1_genomic.fna/markers.fasta)
[2023-06-29 13:00:30,390] [INFO] Task started: Blastn
[2023-06-29 13:00:30,390] [INFO] Running command: blastn -query GCA_020072595.1_ASM2007259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec70c3ba-f2fe-415f-b298-18871d9cb402/dqc_reference/reference_markers_gtdb.fasta -out GCA_020072595.1_ASM2007259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:00:31,325] [INFO] Task succeeded: Blastn
[2023-06-29 13:00:31,330] [INFO] Selected 29 target genomes.
[2023-06-29 13:00:31,330] [INFO] Target genome list was writen to GCA_020072595.1_ASM2007259v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:00:31,349] [INFO] Task started: fastANI
[2023-06-29 13:00:31,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg99a7c684-9534-464f-b323-0467060a5920/GCA_020072595.1_ASM2007259v1_genomic.fna.gz --refList GCA_020072595.1_ASM2007259v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020072595.1_ASM2007259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:00:50,340] [INFO] Task succeeded: fastANI
[2023-06-29 13:00:50,365] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:00:50,365] [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_003223515.1	s__Gp1-AA17 sp003223515	76.9693	359	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Gp1-AA117;g__Gp1-AA17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003131315.1	s__Bog-209 sp003131315	76.8811	117	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.89	99.89	0.97	0.97	2	-
GCA_011046795.1	s__DSPA01 sp011046795	76.716	125	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__DSPA01;g__DSPA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185395.1	s__JACPNR01 sp016185395	76.6401	137	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__JACPNR01;g__JACPNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	76.4908	72	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134995.1	s__Sulfotelmatobacter sp003134995	76.3572	96	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	99.91	99.75	0.99	0.98	6	-
GCF_000022565.1	s__Acidobacterium capsulatum	76.3482	84	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003160215.1	s__Bog-257 sp003160215	76.3471	103	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	96.50	96.50	0.80	0.80	2	-
GCA_003151335.1	s__Bog-257 sp003151335	76.3192	122	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	99.88	99.88	0.93	0.93	2	-
GCA_003152695.1	s__Bog-257 sp003152695	76.2093	117	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	99.78	99.24	0.95	0.92	6	-
GCA_003151875.1	s__Bog-257 sp003151875	76.1854	96	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135315.1	s__Bog-257 sp003135315	76.162	71	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003225465.1	s__Gp1-AA133 sp003225465	76.1551	93	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Gp1-AA133	95.0	97.18	95.46	0.82	0.78	3	-
GCA_003132405.1	s__Bog-209 sp003132405	76.1358	85	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.82	99.57	0.92	0.89	8	-
GCA_003135475.1	s__Bog-257 sp003135475	76.1217	89	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123295.1	s__Silvibacterium dinghuense	76.0946	95	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016201265.1	s__QIAJ01 sp016201265	76.0708	98	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__QIAJ01	95.0	99.34	99.34	0.79	0.79	2	-
GCA_903847195.1	s__CAINCZ01 sp903847195	76.0642	63	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__CAINCZ01;g__CAINCZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654835.1	s__Terracidiphilus sp015654835	75.9051	57	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003154055.1	s__QIAJ01 sp003154055	75.8935	94	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__QIAJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164855.1	s__Sulfotelmatobacter sp003164855	75.8167	105	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162935.1	s__Bog-209 sp003162935	75.8135	86	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.71	99.50	0.89	0.82	23	-
GCA_003167255.1	s__PALSA-129 sp003167255	75.7453	74	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PALSA-129	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152795.1	s__Bog-209 sp003152795	75.6738	78	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151435.1	s__Terracidiphilus sp003151435	75.6723	69	2114	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.67	99.67	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-29 13:00:50,367] [INFO] GTDB search result was written to GCA_020072595.1_ASM2007259v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:00:50,369] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:00:50,374] [INFO] DFAST_QC result json was written to GCA_020072595.1_ASM2007259v1_genomic.fna/dqc_result.json
[2023-06-29 13:00:50,374] [INFO] DFAST_QC completed!
[2023-06-29 13:00:50,374] [INFO] Total running time: 0h2m10s