[2023-06-29 19:25:16,032] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:25:16,034] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:25:16,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg565c2506-11eb-43f6-ab99-a51bdc798c42/dqc_reference
[2023-06-29 19:25:17,204] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:25:17,207] [INFO] Task started: Prodigal
[2023-06-29 19:25:17,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg942dd138-2dcf-436e-98c3-0a2ca28bb6a1/GCA_021286685.1_ASM2128668v1_genomic.fna.gz | prodigal -d GCA_021286685.1_ASM2128668v1_genomic.fna/cds.fna -a GCA_021286685.1_ASM2128668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:25:27,493] [INFO] Task succeeded: Prodigal
[2023-06-29 19:25:27,493] [INFO] Task started: HMMsearch
[2023-06-29 19:25:27,493] [INFO] Running command: hmmsearch --tblout GCA_021286685.1_ASM2128668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg565c2506-11eb-43f6-ab99-a51bdc798c42/dqc_reference/reference_markers.hmm GCA_021286685.1_ASM2128668v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:25:27,690] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:25:27,691] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg942dd138-2dcf-436e-98c3-0a2ca28bb6a1/GCA_021286685.1_ASM2128668v1_genomic.fna.gz]
[2023-06-29 19:25:27,719] [INFO] Query marker FASTA was written to GCA_021286685.1_ASM2128668v1_genomic.fna/markers.fasta
[2023-06-29 19:25:27,719] [INFO] Task started: Blastn
[2023-06-29 19:25:27,720] [INFO] Running command: blastn -query GCA_021286685.1_ASM2128668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg565c2506-11eb-43f6-ab99-a51bdc798c42/dqc_reference/reference_markers.fasta -out GCA_021286685.1_ASM2128668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:25:28,324] [INFO] Task succeeded: Blastn
[2023-06-29 19:25:28,329] [INFO] Selected 14 target genomes.
[2023-06-29 19:25:28,330] [INFO] Target genome list was writen to GCA_021286685.1_ASM2128668v1_genomic.fna/target_genomes.txt
[2023-06-29 19:25:28,332] [INFO] Task started: fastANI
[2023-06-29 19:25:28,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg942dd138-2dcf-436e-98c3-0a2ca28bb6a1/GCA_021286685.1_ASM2128668v1_genomic.fna.gz --refList GCA_021286685.1_ASM2128668v1_genomic.fna/target_genomes.txt --output GCA_021286685.1_ASM2128668v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:25:36,290] [INFO] Task succeeded: fastANI
[2023-06-29 19:25:36,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg565c2506-11eb-43f6-ab99-a51bdc798c42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:25:36,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg565c2506-11eb-43f6-ab99-a51bdc798c42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:25:36,301] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:25:36,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:25:36,301] [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
Chlorobaculum limnaeum	strain=DSM 1677	GCA_001747405.1	274537	274537	type	True	79.6327	158	392	95	below_threshold
Chlorobaculum thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	79.0691	156	392	95	below_threshold
Chlorobaculum tepidum	strain=TLS	GCA_000006985.1	1097	1097	type	True	79.0532	143	392	95	below_threshold
Pelodictyon luteolum	strain=DSM 273	GCA_000012485.1	1100	1100	type	True	77.6028	75	392	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.5066	53	392	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:25:36,303] [INFO] DFAST Taxonomy check result was written to GCA_021286685.1_ASM2128668v1_genomic.fna/tc_result.tsv
[2023-06-29 19:25:36,304] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:25:36,304] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:25:36,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg565c2506-11eb-43f6-ab99-a51bdc798c42/dqc_reference/checkm_data
[2023-06-29 19:25:36,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:25:36,332] [INFO] Task started: CheckM
[2023-06-29 19:25:36,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021286685.1_ASM2128668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021286685.1_ASM2128668v1_genomic.fna/checkm_input GCA_021286685.1_ASM2128668v1_genomic.fna/checkm_result
[2023-06-29 19:26:11,232] [INFO] Task succeeded: CheckM
[2023-06-29 19:26:11,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:26:11,254] [INFO] ===== Completeness check finished =====
[2023-06-29 19:26:11,255] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:26:11,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021286685.1_ASM2128668v1_genomic.fna/markers.fasta)
[2023-06-29 19:26:11,255] [INFO] Task started: Blastn
[2023-06-29 19:26:11,255] [INFO] Running command: blastn -query GCA_021286685.1_ASM2128668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg565c2506-11eb-43f6-ab99-a51bdc798c42/dqc_reference/reference_markers_gtdb.fasta -out GCA_021286685.1_ASM2128668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:26:12,101] [INFO] Task succeeded: Blastn
[2023-06-29 19:26:12,106] [INFO] Selected 9 target genomes.
[2023-06-29 19:26:12,107] [INFO] Target genome list was writen to GCA_021286685.1_ASM2128668v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:26:12,112] [INFO] Task started: fastANI
[2023-06-29 19:26:12,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg942dd138-2dcf-436e-98c3-0a2ca28bb6a1/GCA_021286685.1_ASM2128668v1_genomic.fna.gz --refList GCA_021286685.1_ASM2128668v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021286685.1_ASM2128668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:26:15,621] [INFO] Task succeeded: fastANI
[2023-06-29 19:26:15,633] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:26:15,633] [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_013334925.1	s__Chlorobaculum sp013334925	98.1889	353	392	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	99.14	99.14	0.90	0.90	2	conclusive
GCA_900299075.1	s__Chlorobaculum sp900299075	81.2301	179	392	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334865.1	s__Chlorobaculum sp013334865	81.0275	194	392	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334335.1	s__Chlorobaculum sp013334335	80.6928	214	392	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	99.81	99.81	0.89	0.89	2	-
GCA_013335115.1	s__Chlorobaculum sp013335115	80.4342	195	392	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929135.1	s__Chlorobaculum sp903929135	80.2849	191	392	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	99.99	99.99	0.95	0.95	2	-
GCA_016931495.1	s__Chlorobaculum sp016931495	79.712	133	392	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001602925.1	s__Chlorobaculum sp001602925	79.3933	145	392	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000006985.1	s__Chlorobaculum tepidum	79.0532	143	392	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-29 19:26:15,635] [INFO] GTDB search result was written to GCA_021286685.1_ASM2128668v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:26:15,636] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:26:15,639] [INFO] DFAST_QC result json was written to GCA_021286685.1_ASM2128668v1_genomic.fna/dqc_result.json
[2023-06-29 19:26:15,639] [INFO] DFAST_QC completed!
[2023-06-29 19:26:15,639] [INFO] Total running time: 0h0m60s