[2024-01-24 14:19:16,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:16,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:16,118] [INFO] DQC Reference Directory: /var/lib/cwl/stgca67be89-2898-4085-beae-aaa10086cc2c/dqc_reference
[2024-01-24 14:19:17,391] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:17,391] [INFO] Task started: Prodigal
[2024-01-24 14:19:17,392] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9561338-c515-47a2-8cb9-ea7b5eb325da/GCF_009834785.1_ASM983478v1_genomic.fna.gz | prodigal -d GCF_009834785.1_ASM983478v1_genomic.fna/cds.fna -a GCF_009834785.1_ASM983478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:38,283] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:38,284] [INFO] Task started: HMMsearch
[2024-01-24 14:19:38,284] [INFO] Running command: hmmsearch --tblout GCF_009834785.1_ASM983478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca67be89-2898-4085-beae-aaa10086cc2c/dqc_reference/reference_markers.hmm GCF_009834785.1_ASM983478v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:38,593] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:38,625] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc9561338-c515-47a2-8cb9-ea7b5eb325da/GCF_009834785.1_ASM983478v1_genomic.fna.gz]
[2024-01-24 14:19:38,672] [INFO] Query marker FASTA was written to GCF_009834785.1_ASM983478v1_genomic.fna/markers.fasta
[2024-01-24 14:19:38,673] [INFO] Task started: Blastn
[2024-01-24 14:19:38,673] [INFO] Running command: blastn -query GCF_009834785.1_ASM983478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca67be89-2898-4085-beae-aaa10086cc2c/dqc_reference/reference_markers.fasta -out GCF_009834785.1_ASM983478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:39,502] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:39,506] [INFO] Selected 10 target genomes.
[2024-01-24 14:19:39,506] [INFO] Target genome list was writen to GCF_009834785.1_ASM983478v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:39,515] [INFO] Task started: fastANI
[2024-01-24 14:19:39,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9561338-c515-47a2-8cb9-ea7b5eb325da/GCF_009834785.1_ASM983478v1_genomic.fna.gz --refList GCF_009834785.1_ASM983478v1_genomic.fna/target_genomes.txt --output GCF_009834785.1_ASM983478v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:53,297] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:53,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca67be89-2898-4085-beae-aaa10086cc2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:53,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca67be89-2898-4085-beae-aaa10086cc2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:53,316] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:53,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:53,317] [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
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	100.0	1481	1485	95	conclusive
Natronorubrum halophilum	strain=SHR37	GCA_003670115.1	1702106	1702106	type	True	83.002	902	1485	95	below_threshold
Natronorubrum tibetense	strain=GA33	GCA_000383975.1	63128	63128	type	True	82.8173	985	1485	95	below_threshold
Natronorubrum tibetense	strain=GA33	GCA_000337235.1	63128	63128	type	True	82.7634	967	1485	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	82.2736	851	1485	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	81.9572	871	1485	95	below_threshold
Natronorubrum aibiense	strain=7-3	GCA_009392895.1	348826	348826	type	True	81.7268	795	1485	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	80.8655	682	1485	95	below_threshold
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	80.8367	693	1485	95	below_threshold
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	80.6634	662	1485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:53,318] [INFO] DFAST Taxonomy check result was written to GCF_009834785.1_ASM983478v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:53,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:53,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:53,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca67be89-2898-4085-beae-aaa10086cc2c/dqc_reference/checkm_data
[2024-01-24 14:19:53,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:53,390] [INFO] Task started: CheckM
[2024-01-24 14:19:53,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009834785.1_ASM983478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009834785.1_ASM983478v1_genomic.fna/checkm_input GCF_009834785.1_ASM983478v1_genomic.fna/checkm_result
[2024-01-24 14:20:57,434] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:57,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:57,461] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:57,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:57,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009834785.1_ASM983478v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:57,463] [INFO] Task started: Blastn
[2024-01-24 14:20:57,463] [INFO] Running command: blastn -query GCF_009834785.1_ASM983478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca67be89-2898-4085-beae-aaa10086cc2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009834785.1_ASM983478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:58,072] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:58,101] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:58,101] [INFO] Target genome list was writen to GCF_009834785.1_ASM983478v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:58,118] [INFO] Task started: fastANI
[2024-01-24 14:20:58,118] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9561338-c515-47a2-8cb9-ea7b5eb325da/GCF_009834785.1_ASM983478v1_genomic.fna.gz --refList GCF_009834785.1_ASM983478v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009834785.1_ASM983478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:09,264] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:09,280] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:09,280] [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_009834785.1	s__Natronorubrum halalkaliphilum	100.0	1481	1485	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900100335.1	s__Natronorubrum texcoconense	83.0015	977	1485	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	82.9856	905	1485	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	97.42	97.42	0.91	0.91	2	-
GCF_000383975.1	s__Natronorubrum tibetense	82.7803	990	1485	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017352155.1	s__Haloterrigena sp017352155	82.4223	799	1485	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	82.202	880	1485	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_000337215.1	s__Natronolimnohabitans innermongolicus	81.8051	872	1485	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009392895.1	s__Natronorubrum aibiense	81.7207	796	1485	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013456555.1	s__Natrinema sp013456555	81.0404	740	1485	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337615.1	s__Natrinema pallidum	80.6821	659	1485	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.94	98.94	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:09,282] [INFO] GTDB search result was written to GCF_009834785.1_ASM983478v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:09,282] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:09,285] [INFO] DFAST_QC result json was written to GCF_009834785.1_ASM983478v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:09,285] [INFO] DFAST_QC completed!
[2024-01-24 14:21:09,286] [INFO] Total running time: 0h1m53s