[2024-01-25 19:49:35,566] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:35,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:35,568] [INFO] DQC Reference Directory: /var/lib/cwl/stgb638d85e-d57c-411c-b7b6-f92a9ae83e80/dqc_reference
[2024-01-25 19:49:36,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:36,683] [INFO] Task started: Prodigal
[2024-01-25 19:49:36,684] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d15b11f-950b-45b8-b631-04b3229ab895/GCF_025685625.1_ASM2568562v1_genomic.fna.gz | prodigal -d GCF_025685625.1_ASM2568562v1_genomic.fna/cds.fna -a GCF_025685625.1_ASM2568562v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:55,502] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:55,502] [INFO] Task started: HMMsearch
[2024-01-25 19:49:55,502] [INFO] Running command: hmmsearch --tblout GCF_025685625.1_ASM2568562v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb638d85e-d57c-411c-b7b6-f92a9ae83e80/dqc_reference/reference_markers.hmm GCF_025685625.1_ASM2568562v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:55,786] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:55,787] [INFO] Found 6/6 markers.
[2024-01-25 19:49:55,840] [INFO] Query marker FASTA was written to GCF_025685625.1_ASM2568562v1_genomic.fna/markers.fasta
[2024-01-25 19:49:55,841] [INFO] Task started: Blastn
[2024-01-25 19:49:55,841] [INFO] Running command: blastn -query GCF_025685625.1_ASM2568562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb638d85e-d57c-411c-b7b6-f92a9ae83e80/dqc_reference/reference_markers.fasta -out GCF_025685625.1_ASM2568562v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:56,413] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:56,421] [INFO] Selected 23 target genomes.
[2024-01-25 19:49:56,422] [INFO] Target genome list was writen to GCF_025685625.1_ASM2568562v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:56,451] [INFO] Task started: fastANI
[2024-01-25 19:49:56,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d15b11f-950b-45b8-b631-04b3229ab895/GCF_025685625.1_ASM2568562v1_genomic.fna.gz --refList GCF_025685625.1_ASM2568562v1_genomic.fna/target_genomes.txt --output GCF_025685625.1_ASM2568562v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:19,766] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:19,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb638d85e-d57c-411c-b7b6-f92a9ae83e80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:19,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb638d85e-d57c-411c-b7b6-f92a9ae83e80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:19,777] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:50:19,777] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:50:19,777] [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
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	78.2913	168	2364	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	77.6642	209	2364	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	77.4028	132	2364	95	below_threshold
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	77.3702	232	2364	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	77.348	137	2364	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.1152	118	2364	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	77.057	186	2364	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.9651	166	2364	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.9418	230	2364	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.9201	139	2364	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.8993	231	2364	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	76.8967	199	2364	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.8725	167	2364	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	76.847	140	2364	95	below_threshold
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	76.654	97	2364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:19,778] [INFO] DFAST Taxonomy check result was written to GCF_025685625.1_ASM2568562v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:19,778] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:19,779] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:19,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb638d85e-d57c-411c-b7b6-f92a9ae83e80/dqc_reference/checkm_data
[2024-01-25 19:50:19,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:19,847] [INFO] Task started: CheckM
[2024-01-25 19:50:19,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685625.1_ASM2568562v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685625.1_ASM2568562v1_genomic.fna/checkm_input GCF_025685625.1_ASM2568562v1_genomic.fna/checkm_result
[2024-01-25 19:51:12,264] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:12,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:12,282] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:12,282] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:12,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685625.1_ASM2568562v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:12,283] [INFO] Task started: Blastn
[2024-01-25 19:51:12,283] [INFO] Running command: blastn -query GCF_025685625.1_ASM2568562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb638d85e-d57c-411c-b7b6-f92a9ae83e80/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685625.1_ASM2568562v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:13,118] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:13,121] [INFO] Selected 24 target genomes.
[2024-01-25 19:51:13,121] [INFO] Target genome list was writen to GCF_025685625.1_ASM2568562v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:13,158] [INFO] Task started: fastANI
[2024-01-25 19:51:13,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d15b11f-950b-45b8-b631-04b3229ab895/GCF_025685625.1_ASM2568562v1_genomic.fna.gz --refList GCF_025685625.1_ASM2568562v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685625.1_ASM2568562v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:32,317] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:32,327] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:51:32,328] [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_903832055.1	s__CAIVDV01 sp903832055	78.5197	427	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	100.00	100.00	0.99	0.99	4	-
GCA_903832475.1	s__CAIVDV01 sp903832475	78.0709	346	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	98.66	98.66	0.84	0.84	2	-
GCF_001449115.1	s__Terracidiphilus gabretensis	77.3702	232	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904755.1	s__CAIVDV01 sp903904755	77.3058	275	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	99.92	99.89	0.96	0.95	6	-
GCA_000620725.1	s__Terracidiphilus sp000620725	77.1209	210	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903849645.1	s__Terracidiphilus sp903849645	77.1082	249	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003428625.2	s__Palsa-343 sp003428625	77.0695	185	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008682415.1	s__Terracidiphilus sp008682415	76.9811	228	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828675.1	s__Terracidiphilus sp903828675	76.9617	196	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.87	99.75	0.95	0.93	4	-
GCF_001006305.1	s__Silvibacterium bohemicum	76.932	231	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003134855.1	s__Terracidiphilus sp003134855	76.7994	195	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873705.1	s__CAIQPK01 sp903873705	76.7862	107	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIQPK01	95.0	99.92	99.91	0.95	0.94	3	-
GCA_003138515.1	s__Terracidiphilus sp003138515	76.7763	153	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.80	99.73	0.97	0.96	5	-
GCA_003151435.1	s__Terracidiphilus sp003151435	76.7031	216	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.67	99.67	0.90	0.90	2	-
GCA_003167305.1	s__Terracidiphilus sp003167305	76.6383	140	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003159355.1	s__Terracidiphilus sp003159355	76.3215	164	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.48	99.30	0.83	0.80	7	-
GCF_900290245.1	s__Terracidiphilus gaucii	76.2528	162	2364	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:32,329] [INFO] GTDB search result was written to GCF_025685625.1_ASM2568562v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:32,329] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:32,333] [INFO] DFAST_QC result json was written to GCF_025685625.1_ASM2568562v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:32,333] [INFO] DFAST_QC completed!
[2024-01-25 19:51:32,333] [INFO] Total running time: 0h1m57s