[2024-01-24 15:18:47,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:47,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:47,940] [INFO] DQC Reference Directory: /var/lib/cwl/stgdce04611-a71e-4fc4-8c94-d116cdbdcc50/dqc_reference
[2024-01-24 15:18:51,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:51,761] [INFO] Task started: Prodigal
[2024-01-24 15:18:51,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg134a3c4c-d37d-4470-b51a-49b3f58a42c9/GCF_001449115.1_ASM144911v1_genomic.fna.gz | prodigal -d GCF_001449115.1_ASM144911v1_genomic.fna/cds.fna -a GCF_001449115.1_ASM144911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:07,500] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:07,500] [INFO] Task started: HMMsearch
[2024-01-24 15:19:07,501] [INFO] Running command: hmmsearch --tblout GCF_001449115.1_ASM144911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdce04611-a71e-4fc4-8c94-d116cdbdcc50/dqc_reference/reference_markers.hmm GCF_001449115.1_ASM144911v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:07,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:07,783] [INFO] Found 6/6 markers.
[2024-01-24 15:19:07,828] [INFO] Query marker FASTA was written to GCF_001449115.1_ASM144911v1_genomic.fna/markers.fasta
[2024-01-24 15:19:07,829] [INFO] Task started: Blastn
[2024-01-24 15:19:07,829] [INFO] Running command: blastn -query GCF_001449115.1_ASM144911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdce04611-a71e-4fc4-8c94-d116cdbdcc50/dqc_reference/reference_markers.fasta -out GCF_001449115.1_ASM144911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:08,434] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:08,438] [INFO] Selected 17 target genomes.
[2024-01-24 15:19:08,438] [INFO] Target genome list was writen to GCF_001449115.1_ASM144911v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:08,560] [INFO] Task started: fastANI
[2024-01-24 15:19:08,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg134a3c4c-d37d-4470-b51a-49b3f58a42c9/GCF_001449115.1_ASM144911v1_genomic.fna.gz --refList GCF_001449115.1_ASM144911v1_genomic.fna/target_genomes.txt --output GCF_001449115.1_ASM144911v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:23,657] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:23,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdce04611-a71e-4fc4-8c94-d116cdbdcc50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:23,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdce04611-a71e-4fc4-8c94-d116cdbdcc50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:23,677] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:23,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:23,677] [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
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	100.0	1773	1776	95	conclusive
Acidisarcina polymorpha	strain=SBC82	GCA_003330725.1	2211140	2211140	type	True	79.2189	101	1776	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	77.3924	320	1776	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.329	130	1776	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	77.1074	165	1776	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	77.106	163	1776	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	76.9335	111	1776	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	76.9049	126	1776	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	76.8945	114	1776	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.894	155	1776	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	76.8742	139	1776	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.7768	168	1776	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.7033	178	1776	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.6768	164	1776	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:23,679] [INFO] DFAST Taxonomy check result was written to GCF_001449115.1_ASM144911v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:23,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:23,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:23,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdce04611-a71e-4fc4-8c94-d116cdbdcc50/dqc_reference/checkm_data
[2024-01-24 15:19:23,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:23,730] [INFO] Task started: CheckM
[2024-01-24 15:19:23,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001449115.1_ASM144911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001449115.1_ASM144911v1_genomic.fna/checkm_input GCF_001449115.1_ASM144911v1_genomic.fna/checkm_result
[2024-01-24 15:20:10,485] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:10,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:10,511] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:10,511] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:10,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001449115.1_ASM144911v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:10,512] [INFO] Task started: Blastn
[2024-01-24 15:20:10,512] [INFO] Running command: blastn -query GCF_001449115.1_ASM144911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdce04611-a71e-4fc4-8c94-d116cdbdcc50/dqc_reference/reference_markers_gtdb.fasta -out GCF_001449115.1_ASM144911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:11,339] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:11,344] [INFO] Selected 18 target genomes.
[2024-01-24 15:20:11,344] [INFO] Target genome list was writen to GCF_001449115.1_ASM144911v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:11,358] [INFO] Task started: fastANI
[2024-01-24 15:20:11,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg134a3c4c-d37d-4470-b51a-49b3f58a42c9/GCF_001449115.1_ASM144911v1_genomic.fna.gz --refList GCF_001449115.1_ASM144911v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001449115.1_ASM144911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:28,726] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:28,741] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:28,741] [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_001449115.1	s__Terracidiphilus gabretensis	100.0	1773	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015655195.1	s__Terracidiphilus sp015655195	78.2087	502	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620725.1	s__Terracidiphilus sp000620725	77.437	275	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285705.1	s__Acidobacterium_A sp013285705	77.3881	82	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008682415.1	s__Terracidiphilus sp008682415	77.3085	314	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151435.1	s__Terracidiphilus sp003151435	77.1676	276	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.67	99.67	0.90	0.90	2	-
GCA_003134815.1	s__Terracidiphilus sp003134815	77.1578	184	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003131205.1	s__Terracidiphilus savannae	77.1251	226	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142015.1	s__Terracidiphilus sp003142015	77.0505	176	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.69	99.69	0.91	0.91	2	-
GCA_003142935.1	s__Terracidiphilus sp003142935	77.0362	227	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.68	99.68	0.90	0.90	2	-
GCA_018268915.1	s__Terracidiphilus sp018268915	77.035	193	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654835.1	s__Terracidiphilus sp015654835	76.9831	221	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165075.1	s__Terracidiphilus sp003165075	76.9689	191	1776	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	76.8628	222	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.87	99.75	0.95	0.93	4	-
GCA_903911925.1	s__Terracidiphilus sp903911925	76.7986	223	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162495.1	s__Terracidiphilus sp003162495	76.6234	163	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140785.1	s__Terracidiphilus sp003140785	76.405	182	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	98.14	96.92	0.80	0.78	3	-
GCA_003165935.1	s__Terracidiphilus sp003165935	76.4014	180	1776	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:28,743] [INFO] GTDB search result was written to GCF_001449115.1_ASM144911v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:28,743] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:28,747] [INFO] DFAST_QC result json was written to GCF_001449115.1_ASM144911v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:28,748] [INFO] DFAST_QC completed!
[2024-01-24 15:20:28,748] [INFO] Total running time: 0h1m41s