[2024-01-24 13:21:58,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:58,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:58,925] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9e3bfc8-e32d-49ab-b51f-9838ee48038c/dqc_reference
[2024-01-24 13:22:00,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:00,214] [INFO] Task started: Prodigal
[2024-01-24 13:22:00,214] [INFO] Running command: gunzip -c /var/lib/cwl/stgc475c12d-5001-4e8d-9852-7c1d9cfdf433/GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/cds.fna -a GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:20,312] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:20,312] [INFO] Task started: HMMsearch
[2024-01-24 13:22:20,312] [INFO] Running command: hmmsearch --tblout GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9e3bfc8-e32d-49ab-b51f-9838ee48038c/dqc_reference/reference_markers.hmm GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:20,602] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:20,603] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc475c12d-5001-4e8d-9852-7c1d9cfdf433/GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna.gz]
[2024-01-24 13:22:20,647] [INFO] Query marker FASTA was written to GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:20,647] [INFO] Task started: Blastn
[2024-01-24 13:22:20,647] [INFO] Running command: blastn -query GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e3bfc8-e32d-49ab-b51f-9838ee48038c/dqc_reference/reference_markers.fasta -out GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:21,193] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:21,196] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:21,196] [INFO] Target genome list was writen to GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:21,203] [INFO] Task started: fastANI
[2024-01-24 13:22:21,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgc475c12d-5001-4e8d-9852-7c1d9cfdf433/GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna.gz --refList GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:33,376] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:33,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9e3bfc8-e32d-49ab-b51f-9838ee48038c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:33,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9e3bfc8-e32d-49ab-b51f-9838ee48038c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:33,394] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:33,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:33,394] [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
Haloterrigena daqingensis	strain=CGMCC 1.8909	GCA_900156445.1	588898	588898	type	True	100.0	1268	1270	95	conclusive
Haloterrigena daqingensis	strain=JX313	GCA_001971705.1	588898	588898	type	True	99.999	1268	1270	95	conclusive
Natronorubrum tibetense	strain=GA33	GCA_000383975.1	63128	63128	type	True	81.3587	827	1270	95	below_threshold
Natronorubrum halophilum	strain=SHR37	GCA_003670115.1	1702106	1702106	type	True	81.0901	747	1270	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	80.8959	741	1270	95	below_threshold
Natronorubrum sulfidifaciens	strain=JCM 14089	GCA_000337735.1	388259	388259	type	True	80.8236	629	1270	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	80.7398	736	1270	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	80.4015	710	1270	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	80.0756	687	1270	95	below_threshold
Natrialba hulunbeirensis	strain=JCM 10989	GCA_000337575.1	123783	123783	type	True	80.0684	610	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:33,396] [INFO] DFAST Taxonomy check result was written to GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:33,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:33,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:33,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9e3bfc8-e32d-49ab-b51f-9838ee48038c/dqc_reference/checkm_data
[2024-01-24 13:22:33,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:33,438] [INFO] Task started: CheckM
[2024-01-24 13:22:33,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/checkm_input GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:28,690] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:28,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:28,711] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:28,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:28,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:28,712] [INFO] Task started: Blastn
[2024-01-24 13:23:28,712] [INFO] Running command: blastn -query GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e3bfc8-e32d-49ab-b51f-9838ee48038c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:29,256] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:29,261] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:29,261] [INFO] Target genome list was writen to GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:29,280] [INFO] Task started: fastANI
[2024-01-24 13:23:29,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgc475c12d-5001-4e8d-9852-7c1d9cfdf433/GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna.gz --refList GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:39,090] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:39,099] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:39,099] [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_001971705.1	s__Natronorubrum daqingense	99.999	1268	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900108095.1	s__Natronorubrum sediminis	94.2655	1090	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100335.1	s__Natronorubrum texcoconense	81.7903	843	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670115.1	s__Natronorubrum sp003670115	81.0726	749	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	97.42	97.42	0.91	0.91	2	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	80.9068	739	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	80.8229	698	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013342135.1	s__Haloterrigena sp013342135	80.7717	740	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_001861355.1	s__Natrialba sp001861355	80.2584	623	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122205.1	s__Natronococcus sp008122205	80.0924	683	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337575.1	s__Natrialba hulunbeirensis	80.0741	609	1270	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:39,215] [INFO] GTDB search result was written to GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:39,216] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:39,221] [INFO] DFAST_QC result json was written to GCF_900156445.1_IMG-taxon_2681812915_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:39,221] [INFO] DFAST_QC completed!
[2024-01-24 13:23:39,221] [INFO] Total running time: 0h1m40s