[2023-06-29 10:49:34,593] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:49:34,598] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:49:34,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgd33e7e1e-1192-4aae-b7fc-d59ae851d70e/dqc_reference
[2023-06-29 10:49:36,073] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:49:36,074] [INFO] Task started: Prodigal
[2023-06-29 10:49:36,074] [INFO] Running command: gunzip -c /var/lib/cwl/stgf40f34ef-144d-40ee-a534-9278fa872b1e/GCA_020072815.1_ASM2007281v1_genomic.fna.gz | prodigal -d GCA_020072815.1_ASM2007281v1_genomic.fna/cds.fna -a GCA_020072815.1_ASM2007281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:49:52,973] [INFO] Task succeeded: Prodigal
[2023-06-29 10:49:52,973] [INFO] Task started: HMMsearch
[2023-06-29 10:49:52,974] [INFO] Running command: hmmsearch --tblout GCA_020072815.1_ASM2007281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd33e7e1e-1192-4aae-b7fc-d59ae851d70e/dqc_reference/reference_markers.hmm GCA_020072815.1_ASM2007281v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:49:53,271] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:49:53,272] [INFO] Found 6/6 markers.
[2023-06-29 10:49:53,313] [INFO] Query marker FASTA was written to GCA_020072815.1_ASM2007281v1_genomic.fna/markers.fasta
[2023-06-29 10:49:53,314] [INFO] Task started: Blastn
[2023-06-29 10:49:53,314] [INFO] Running command: blastn -query GCA_020072815.1_ASM2007281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd33e7e1e-1192-4aae-b7fc-d59ae851d70e/dqc_reference/reference_markers.fasta -out GCA_020072815.1_ASM2007281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:49:53,935] [INFO] Task succeeded: Blastn
[2023-06-29 10:49:53,939] [INFO] Selected 22 target genomes.
[2023-06-29 10:49:53,940] [INFO] Target genome list was writen to GCA_020072815.1_ASM2007281v1_genomic.fna/target_genomes.txt
[2023-06-29 10:49:53,942] [INFO] Task started: fastANI
[2023-06-29 10:49:53,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgf40f34ef-144d-40ee-a534-9278fa872b1e/GCA_020072815.1_ASM2007281v1_genomic.fna.gz --refList GCA_020072815.1_ASM2007281v1_genomic.fna/target_genomes.txt --output GCA_020072815.1_ASM2007281v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:50:09,054] [INFO] Task succeeded: fastANI
[2023-06-29 10:50:09,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd33e7e1e-1192-4aae-b7fc-d59ae851d70e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:50:09,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd33e7e1e-1192-4aae-b7fc-d59ae851d70e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:50:09,064] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:50:09,064] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 10:50:09,064] [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
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	76.3382	72	1749	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.2594	77	1749	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.1012	76	1749	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.0786	77	1749	95	below_threshold
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	75.934	56	1749	95	below_threshold
Pseudacidobacterium ailaaui	strain=PMMR2	GCA_000688455.1	1382359	1382359	type	True	75.7523	59	1749	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	75.6371	53	1749	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	74.9963	50	1749	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	74.9246	56	1749	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 10:50:09,066] [INFO] DFAST Taxonomy check result was written to GCA_020072815.1_ASM2007281v1_genomic.fna/tc_result.tsv
[2023-06-29 10:50:09,067] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:50:09,067] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:50:09,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd33e7e1e-1192-4aae-b7fc-d59ae851d70e/dqc_reference/checkm_data
[2023-06-29 10:50:09,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:50:09,121] [INFO] Task started: CheckM
[2023-06-29 10:50:09,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020072815.1_ASM2007281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020072815.1_ASM2007281v1_genomic.fna/checkm_input GCA_020072815.1_ASM2007281v1_genomic.fna/checkm_result
[2023-06-29 10:50:58,048] [INFO] Task succeeded: CheckM
[2023-06-29 10:50:58,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 10:50:58,072] [INFO] ===== Completeness check finished =====
[2023-06-29 10:50:58,072] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:50:58,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020072815.1_ASM2007281v1_genomic.fna/markers.fasta)
[2023-06-29 10:50:58,073] [INFO] Task started: Blastn
[2023-06-29 10:50:58,073] [INFO] Running command: blastn -query GCA_020072815.1_ASM2007281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd33e7e1e-1192-4aae-b7fc-d59ae851d70e/dqc_reference/reference_markers_gtdb.fasta -out GCA_020072815.1_ASM2007281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:50:58,940] [INFO] Task succeeded: Blastn
[2023-06-29 10:50:58,945] [INFO] Selected 23 target genomes.
[2023-06-29 10:50:58,946] [INFO] Target genome list was writen to GCA_020072815.1_ASM2007281v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:50:58,954] [INFO] Task started: fastANI
[2023-06-29 10:50:58,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgf40f34ef-144d-40ee-a534-9278fa872b1e/GCA_020072815.1_ASM2007281v1_genomic.fna.gz --refList GCA_020072815.1_ASM2007281v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020072815.1_ASM2007281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:51:15,856] [INFO] Task succeeded: fastANI
[2023-06-29 10:51:15,880] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 10:51:15,881] [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_011046795.1	s__DSPA01 sp011046795	77.094	162	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__DSPA01;g__DSPA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223515.1	s__Gp1-AA17 sp003223515	77.0182	330	1749	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_003140235.1	s__Gp1-AA17 sp003140235	76.9087	330	1749	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_016185395.1	s__JACPNR01 sp016185395	76.7089	156	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__JACPNR01;g__JACPNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019244045.1	s__Gp1-AA122 sp019244045	76.5241	51	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Gp1-AA122	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151335.1	s__Bog-257 sp003151335	76.4885	141	1749	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_018268755.1	s__KAN-5 sp018268755	76.4039	162	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__KAN-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135475.1	s__Bog-257 sp003135475	76.3511	109	1749	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_003131315.1	s__Bog-209 sp003131315	76.2718	129	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.89	99.89	0.97	0.97	2	-
GCF_000022565.1	s__Acidobacterium capsulatum	76.2594	77	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003131585.1	s__Sulfotelmatobacter sp003131585	76.2536	104	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	99.89	99.89	0.95	0.95	2	-
GCA_003152695.1	s__Bog-257 sp003152695	76.2295	133	1749	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_000381585.1	s__KBS-83 sp000381585	76.1463	65	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__KBS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883425.1	s__Sulfotelmatobacter sp017883425	76.1288	119	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138975.1	s__Sulfotelmatobacter sp003138975	76.0963	95	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151875.1	s__Bog-257 sp003151875	76.0277	100	1749	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_003139995.1	s__Bog-209 sp003139995	75.7823	103	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.91	99.89	0.95	0.94	6	-
GCA_003164855.1	s__Sulfotelmatobacter sp003164855	75.772	84	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019243475.1	s__Gp1-AA112 sp019243475	75.7644	74	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Gp1-AA112;g__Gp1-AA112	95.0	98.96	98.93	0.84	0.83	3	-
GCA_903873705.1	s__CAIQPK01 sp903873705	75.6071	50	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIQPK01	95.0	99.92	99.91	0.95	0.94	3	-
GCA_003166475.1	s__Bog-159 sp003166475	75.5658	71	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bog-159	95.0	99.58	99.43	0.89	0.86	9	-
GCA_018268835.1	s__Solibacter sp018268835	75.4971	79	1749	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Solibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 10:51:15,883] [INFO] GTDB search result was written to GCA_020072815.1_ASM2007281v1_genomic.fna/result_gtdb.tsv
[2023-06-29 10:51:15,883] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:51:15,887] [INFO] DFAST_QC result json was written to GCA_020072815.1_ASM2007281v1_genomic.fna/dqc_result.json
[2023-06-29 10:51:15,887] [INFO] DFAST_QC completed!
[2023-06-29 10:51:15,888] [INFO] Total running time: 0h1m41s