[2024-01-24 12:30:48,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:48,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:48,012] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd0361c4-610d-4e42-8e9e-7c5ada04b822/dqc_reference
[2024-01-24 12:30:49,259] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:49,260] [INFO] Task started: Prodigal
[2024-01-24 12:30:49,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg5433cc71-c8f6-4e64-853a-020452768907/GCF_000337515.1_ASM33751v1_genomic.fna.gz | prodigal -d GCF_000337515.1_ASM33751v1_genomic.fna/cds.fna -a GCF_000337515.1_ASM33751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:02,494] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:02,494] [INFO] Task started: HMMsearch
[2024-01-24 12:31:02,494] [INFO] Running command: hmmsearch --tblout GCF_000337515.1_ASM33751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd0361c4-610d-4e42-8e9e-7c5ada04b822/dqc_reference/reference_markers.hmm GCF_000337515.1_ASM33751v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:02,764] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:02,765] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5433cc71-c8f6-4e64-853a-020452768907/GCF_000337515.1_ASM33751v1_genomic.fna.gz]
[2024-01-24 12:31:02,799] [INFO] Query marker FASTA was written to GCF_000337515.1_ASM33751v1_genomic.fna/markers.fasta
[2024-01-24 12:31:02,799] [INFO] Task started: Blastn
[2024-01-24 12:31:02,799] [INFO] Running command: blastn -query GCF_000337515.1_ASM33751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd0361c4-610d-4e42-8e9e-7c5ada04b822/dqc_reference/reference_markers.fasta -out GCF_000337515.1_ASM33751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:03,292] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:03,294] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:03,295] [INFO] Target genome list was writen to GCF_000337515.1_ASM33751v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:03,300] [INFO] Task started: fastANI
[2024-01-24 12:31:03,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg5433cc71-c8f6-4e64-853a-020452768907/GCF_000337515.1_ASM33751v1_genomic.fna.gz --refList GCF_000337515.1_ASM33751v1_genomic.fna/target_genomes.txt --output GCF_000337515.1_ASM33751v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:11,434] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:11,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd0361c4-610d-4e42-8e9e-7c5ada04b822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:11,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd0361c4-610d-4e42-8e9e-7c5ada04b822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:11,442] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:11,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:11,443] [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
Halovivax asiaticus	strain=JCM 14624	GCA_000337515.1	332953	332953	type	True	100.0	1068	1068	95	conclusive
Halovivax ruber	strain=XH-70	GCA_000328525.1	387341	387341	type	True	93.2822	887	1068	95	below_threshold
Halovivax cerinus	strain=IBRC-M 10256	GCA_024498195.1	1487865	1487865	type	True	84.02	778	1068	95	below_threshold
Halovivax limisalsi	strain=IBRC-M 10022	GCA_023093535.1	1453760	1453760	type	True	81.2586	659	1068	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	78.8312	450	1068	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	78.5697	448	1068	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_002855455.1	44930	44930	type	True	78.0348	322	1068	95	below_threshold
Haloterrigena daqingensis	strain=JX313	GCA_001971705.1	588898	588898	type	True	78.0105	357	1068	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_900114025.1	44930	44930	type	True	77.9609	334	1068	95	below_threshold
Halorubrum lacusprofundi	strain=ATCC 49239	GCA_000022205.1	2247	2247	type	True	76.9405	224	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:11,444] [INFO] DFAST Taxonomy check result was written to GCF_000337515.1_ASM33751v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:11,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:11,444] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:11,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd0361c4-610d-4e42-8e9e-7c5ada04b822/dqc_reference/checkm_data
[2024-01-24 12:31:11,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:11,478] [INFO] Task started: CheckM
[2024-01-24 12:31:11,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337515.1_ASM33751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337515.1_ASM33751v1_genomic.fna/checkm_input GCF_000337515.1_ASM33751v1_genomic.fna/checkm_result
[2024-01-24 12:31:48,923] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:48,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:48,940] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:48,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:48,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337515.1_ASM33751v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:48,941] [INFO] Task started: Blastn
[2024-01-24 12:31:48,941] [INFO] Running command: blastn -query GCF_000337515.1_ASM33751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd0361c4-610d-4e42-8e9e-7c5ada04b822/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337515.1_ASM33751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:49,430] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:49,433] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:49,434] [INFO] Target genome list was writen to GCF_000337515.1_ASM33751v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:49,440] [INFO] Task started: fastANI
[2024-01-24 12:31:49,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg5433cc71-c8f6-4e64-853a-020452768907/GCF_000337515.1_ASM33751v1_genomic.fna.gz --refList GCF_000337515.1_ASM33751v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337515.1_ASM33751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:57,897] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:57,904] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:57,905] [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_000337515.1	s__Halovivax asiaticus	100.0	1068	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000328525.1	s__Halovivax ruber	93.2871	886	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119345.1	s__Halovivax sp007119345	79.3606	456	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	78.9224	434	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455345.1	s__Halopiger_A goleimassiliensis	78.8102	431	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025325.1	s__Haloterrigena turkmenica	78.7133	475	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122205.1	s__Natronococcus sp008122205	78.5838	447	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001563805.1	s__Natrarchaeobaculum sp001563805	78.4994	314	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971705.1	s__Natronorubrum daqingense	78.0366	360	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000022205.1	s__Halorubrum lacusprofundi	76.9611	222	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.55	99.24	0.92	0.87	3	-
GCA_003021085.1	s__PXRE01 sp003021085	76.9237	237	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__PXRE01;g__PXRE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:57,906] [INFO] GTDB search result was written to GCF_000337515.1_ASM33751v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:57,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:57,909] [INFO] DFAST_QC result json was written to GCF_000337515.1_ASM33751v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:57,909] [INFO] DFAST_QC completed!
[2024-01-24 12:31:57,909] [INFO] Total running time: 0h1m10s