[2024-01-25 17:51:35,626] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:35,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:35,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg87ef7b8d-b2a4-4b33-9e8c-c6bffc6f564c/dqc_reference
[2024-01-25 17:51:36,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:36,750] [INFO] Task started: Prodigal
[2024-01-25 17:51:36,750] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f1037f7-9a8b-4a90-a976-fa08ca46585f/GCF_025685415.1_ASM2568541v1_genomic.fna.gz | prodigal -d GCF_025685415.1_ASM2568541v1_genomic.fna/cds.fna -a GCF_025685415.1_ASM2568541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:48,440] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:48,440] [INFO] Task started: HMMsearch
[2024-01-25 17:51:48,440] [INFO] Running command: hmmsearch --tblout GCF_025685415.1_ASM2568541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87ef7b8d-b2a4-4b33-9e8c-c6bffc6f564c/dqc_reference/reference_markers.hmm GCF_025685415.1_ASM2568541v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:48,716] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:48,717] [INFO] Found 6/6 markers.
[2024-01-25 17:51:48,773] [INFO] Query marker FASTA was written to GCF_025685415.1_ASM2568541v1_genomic.fna/markers.fasta
[2024-01-25 17:51:48,773] [INFO] Task started: Blastn
[2024-01-25 17:51:48,774] [INFO] Running command: blastn -query GCF_025685415.1_ASM2568541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87ef7b8d-b2a4-4b33-9e8c-c6bffc6f564c/dqc_reference/reference_markers.fasta -out GCF_025685415.1_ASM2568541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:49,436] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:49,439] [INFO] Selected 18 target genomes.
[2024-01-25 17:51:49,439] [INFO] Target genome list was writen to GCF_025685415.1_ASM2568541v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:49,447] [INFO] Task started: fastANI
[2024-01-25 17:51:49,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f1037f7-9a8b-4a90-a976-fa08ca46585f/GCF_025685415.1_ASM2568541v1_genomic.fna.gz --refList GCF_025685415.1_ASM2568541v1_genomic.fna/target_genomes.txt --output GCF_025685415.1_ASM2568541v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:06,184] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:06,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87ef7b8d-b2a4-4b33-9e8c-c6bffc6f564c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:06,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87ef7b8d-b2a4-4b33-9e8c-c6bffc6f564c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:06,195] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:52:06,195] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:52:06,196] [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
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	78.0643	315	1387	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	77.7327	162	1387	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	77.7265	151	1387	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	77.5169	212	1387	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	77.5149	193	1387	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	77.4487	163	1387	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.4378	211	1387	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	77.395	154	1387	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.376	235	1387	95	below_threshold
Terriglobus saanensis	strain=SP1PR4	GCA_000179915.2	870903	870903	type	True	77.3248	193	1387	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	77.3107	203	1387	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.3008	122	1387	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	77.1582	95	1387	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	77.1363	117	1387	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	77.0639	139	1387	95	below_threshold
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	76.6334	83	1387	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:06,197] [INFO] DFAST Taxonomy check result was written to GCF_025685415.1_ASM2568541v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:06,197] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:06,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:06,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87ef7b8d-b2a4-4b33-9e8c-c6bffc6f564c/dqc_reference/checkm_data
[2024-01-25 17:52:06,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:06,238] [INFO] Task started: CheckM
[2024-01-25 17:52:06,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685415.1_ASM2568541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685415.1_ASM2568541v1_genomic.fna/checkm_input GCF_025685415.1_ASM2568541v1_genomic.fna/checkm_result
[2024-01-25 17:52:41,133] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:41,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:41,154] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:41,154] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:41,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685415.1_ASM2568541v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:41,155] [INFO] Task started: Blastn
[2024-01-25 17:52:41,155] [INFO] Running command: blastn -query GCF_025685415.1_ASM2568541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87ef7b8d-b2a4-4b33-9e8c-c6bffc6f564c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685415.1_ASM2568541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:42,221] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:42,224] [INFO] Selected 13 target genomes.
[2024-01-25 17:52:42,224] [INFO] Target genome list was writen to GCF_025685415.1_ASM2568541v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:42,238] [INFO] Task started: fastANI
[2024-01-25 17:52:42,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f1037f7-9a8b-4a90-a976-fa08ca46585f/GCF_025685415.1_ASM2568541v1_genomic.fna.gz --refList GCF_025685415.1_ASM2568541v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685415.1_ASM2568541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:53,224] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:53,231] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:52:53,232] [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_000265425.1	s__Terriglobus roseus	78.076	314	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102185.1	s__Terriglobus roseus_A	78.0206	227	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105625.1	s__Terriglobus roseus_B	77.9696	301	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800015.1	s__Terriglobus sp000800015	77.9	245	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903642225.1	s__Terriglobus sp903642225	77.6178	271	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640335.1	s__Edaphobacter dinghuensis	77.4487	163	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203225.1	s__Granulicella_A mallensis_A	77.3638	206	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179915.2	s__Terriglobus saanensis	77.3248	193	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970395.1	s__UBA5172 sp903970395	77.1987	143	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903642265.1	s__Granulicella_D sp903642265	76.5557	101	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832475.1	s__CAIVDV01 sp903832475	76.4742	85	1387	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	98.66	98.66	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:53,233] [INFO] GTDB search result was written to GCF_025685415.1_ASM2568541v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:53,234] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:53,237] [INFO] DFAST_QC result json was written to GCF_025685415.1_ASM2568541v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:53,237] [INFO] DFAST_QC completed!
[2024-01-25 17:52:53,237] [INFO] Total running time: 0h1m18s