[2024-01-24 13:55:57,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:57,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:57,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgb162cb5b-9c0e-47c8-ad01-a77be2d7c876/dqc_reference
[2024-01-24 13:55:59,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,099] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b894418-c975-42af-8556-e87bb7c876ab/GCF_008360935.1_ASM836093v1_genomic.fna.gz | prodigal -d GCF_008360935.1_ASM836093v1_genomic.fna/cds.fna -a GCF_008360935.1_ASM836093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:17,636] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:17,637] [INFO] Task started: HMMsearch
[2024-01-24 13:56:17,637] [INFO] Running command: hmmsearch --tblout GCF_008360935.1_ASM836093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb162cb5b-9c0e-47c8-ad01-a77be2d7c876/dqc_reference/reference_markers.hmm GCF_008360935.1_ASM836093v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:17,952] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:17,954] [INFO] Found 6/6 markers.
[2024-01-24 13:56:18,008] [INFO] Query marker FASTA was written to GCF_008360935.1_ASM836093v1_genomic.fna/markers.fasta
[2024-01-24 13:56:18,009] [INFO] Task started: Blastn
[2024-01-24 13:56:18,009] [INFO] Running command: blastn -query GCF_008360935.1_ASM836093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb162cb5b-9c0e-47c8-ad01-a77be2d7c876/dqc_reference/reference_markers.fasta -out GCF_008360935.1_ASM836093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:18,912] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:18,916] [INFO] Selected 14 target genomes.
[2024-01-24 13:56:18,917] [INFO] Target genome list was writen to GCF_008360935.1_ASM836093v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:18,940] [INFO] Task started: fastANI
[2024-01-24 13:56:18,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b894418-c975-42af-8556-e87bb7c876ab/GCF_008360935.1_ASM836093v1_genomic.fna.gz --refList GCF_008360935.1_ASM836093v1_genomic.fna/target_genomes.txt --output GCF_008360935.1_ASM836093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:38,451] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:38,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb162cb5b-9c0e-47c8-ad01-a77be2d7c876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:38,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb162cb5b-9c0e-47c8-ad01-a77be2d7c876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:38,467] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:56:38,467] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:56:38,467] [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
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	83.3076	1299	2156	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	83.2676	1295	2156	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	82.0584	1173	2156	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	81.8802	1159	2156	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	81.6612	1127	2156	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	80.9714	1105	2156	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	80.9649	1144	2156	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	80.2432	857	2156	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.9495	672	2156	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	78.8392	755	2156	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.7413	698	2156	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	78.673	743	2156	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.4811	846	2156	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.8481	746	2156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:38,468] [INFO] DFAST Taxonomy check result was written to GCF_008360935.1_ASM836093v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:38,469] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:38,469] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:38,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb162cb5b-9c0e-47c8-ad01-a77be2d7c876/dqc_reference/checkm_data
[2024-01-24 13:56:38,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:38,531] [INFO] Task started: CheckM
[2024-01-24 13:56:38,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008360935.1_ASM836093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008360935.1_ASM836093v1_genomic.fna/checkm_input GCF_008360935.1_ASM836093v1_genomic.fna/checkm_result
[2024-01-24 13:57:39,249] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:39,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:39,266] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:39,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:39,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008360935.1_ASM836093v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:39,267] [INFO] Task started: Blastn
[2024-01-24 13:57:39,267] [INFO] Running command: blastn -query GCF_008360935.1_ASM836093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb162cb5b-9c0e-47c8-ad01-a77be2d7c876/dqc_reference/reference_markers_gtdb.fasta -out GCF_008360935.1_ASM836093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:41,072] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:41,075] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:41,075] [INFO] Target genome list was writen to GCF_008360935.1_ASM836093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:41,086] [INFO] Task started: fastANI
[2024-01-24 13:57:41,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b894418-c975-42af-8556-e87bb7c876ab/GCF_008360935.1_ASM836093v1_genomic.fna.gz --refList GCF_008360935.1_ASM836093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008360935.1_ASM836093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:11,134] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:11,146] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:11,146] [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_008360935.1	s__Siccirubricoccus phaeus	100.0	2152	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014283215.1	s__Siccirubricoccus deserti	83.3362	1295	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	82.3723	1206	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353985.1	s__Paracraurococcus ruber	82.1295	1165	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	99.87	99.87	0.95	0.95	2	-
GCF_004343615.1	s__Paracraurococcus sp004343615	82.0589	1153	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775475.1	s__Belnapia sp016775475	82.0295	1176	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112485.1	s__Paracraurococcus sp013112485	81.9189	1191	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101615.1	s__Belnapia rosea	81.9109	1154	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	98.36	98.36	0.89	0.89	2	-
GCA_902805545.1	s__Belnapia sp902805545	81.5639	1006	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	81.5236	1097	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802185.1	s__Belnapia sp000802185	81.2589	1077	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355005.1	s__Paracraurococcus ruber_A	81.1944	1208	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016773205.1	s__Belnapia sp016773205	81.0427	1129	2156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,147] [INFO] GTDB search result was written to GCF_008360935.1_ASM836093v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:11,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:11,151] [INFO] DFAST_QC result json was written to GCF_008360935.1_ASM836093v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:11,151] [INFO] DFAST_QC completed!
[2024-01-24 13:58:11,151] [INFO] Total running time: 0h2m13s