[2024-01-25 20:17:50,609] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,611] [INFO] DQC Reference Directory: /var/lib/cwl/stgaafe2472-2867-450d-8512-47390dbeb5e7/dqc_reference
[2024-01-25 20:17:51,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:51,740] [INFO] Task started: Prodigal
[2024-01-25 20:17:51,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg50ec0426-fb73-4c9b-9428-b1aa3b5e9937/GCF_000337475.1_ASM33747v1_genomic.fna.gz | prodigal -d GCF_000337475.1_ASM33747v1_genomic.fna/cds.fna -a GCF_000337475.1_ASM33747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:06,433] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:06,433] [INFO] Task started: HMMsearch
[2024-01-25 20:18:06,433] [INFO] Running command: hmmsearch --tblout GCF_000337475.1_ASM33747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaafe2472-2867-450d-8512-47390dbeb5e7/dqc_reference/reference_markers.hmm GCF_000337475.1_ASM33747v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:06,642] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:06,642] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg50ec0426-fb73-4c9b-9428-b1aa3b5e9937/GCF_000337475.1_ASM33747v1_genomic.fna.gz]
[2024-01-25 20:18:06,672] [INFO] Query marker FASTA was written to GCF_000337475.1_ASM33747v1_genomic.fna/markers.fasta
[2024-01-25 20:18:06,673] [INFO] Task started: Blastn
[2024-01-25 20:18:06,673] [INFO] Running command: blastn -query GCF_000337475.1_ASM33747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaafe2472-2867-450d-8512-47390dbeb5e7/dqc_reference/reference_markers.fasta -out GCF_000337475.1_ASM33747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:07,188] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:07,192] [INFO] Selected 7 target genomes.
[2024-01-25 20:18:07,192] [INFO] Target genome list was writen to GCF_000337475.1_ASM33747v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:07,199] [INFO] Task started: fastANI
[2024-01-25 20:18:07,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ec0426-fb73-4c9b-9428-b1aa3b5e9937/GCF_000337475.1_ASM33747v1_genomic.fna.gz --refList GCF_000337475.1_ASM33747v1_genomic.fna/target_genomes.txt --output GCF_000337475.1_ASM33747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:14,651] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:14,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaafe2472-2867-450d-8512-47390dbeb5e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:14,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaafe2472-2867-450d-8512-47390dbeb5e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:14,657] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:14,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:14,658] [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 limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	100.0	1135	1138	95	conclusive
Haloterrigena hispanica	strain=DSM 18328	GCA_004217335.1	392421	392421	type	True	94.1548	1029	1138	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	83.1192	741	1138	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	82.9742	725	1138	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	82.724	774	1138	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	82.6958	719	1138	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	82.415	709	1138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:14,659] [INFO] DFAST Taxonomy check result was written to GCF_000337475.1_ASM33747v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:14,659] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:14,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:14,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaafe2472-2867-450d-8512-47390dbeb5e7/dqc_reference/checkm_data
[2024-01-25 20:18:14,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:14,697] [INFO] Task started: CheckM
[2024-01-25 20:18:14,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337475.1_ASM33747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337475.1_ASM33747v1_genomic.fna/checkm_input GCF_000337475.1_ASM33747v1_genomic.fna/checkm_result
[2024-01-25 20:18:56,473] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:56,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:56,491] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:56,491] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:56,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337475.1_ASM33747v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:56,492] [INFO] Task started: Blastn
[2024-01-25 20:18:56,492] [INFO] Running command: blastn -query GCF_000337475.1_ASM33747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaafe2472-2867-450d-8512-47390dbeb5e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337475.1_ASM33747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:57,024] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:57,026] [INFO] Selected 7 target genomes.
[2024-01-25 20:18:57,027] [INFO] Target genome list was writen to GCF_000337475.1_ASM33747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:57,031] [INFO] Task started: fastANI
[2024-01-25 20:18:57,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ec0426-fb73-4c9b-9428-b1aa3b5e9937/GCF_000337475.1_ASM33747v1_genomic.fna.gz --refList GCF_000337475.1_ASM33747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337475.1_ASM33747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:04,879] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:04,885] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:04,885] [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_000337475.1	s__Natrinema limicola	100.0	1135	1138	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004217335.1	s__Natrinema hispanicum	94.1837	1026	1138	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111485.1	s__Natrinema hispanicum_A	93.0736	1007	1138	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	99.65	99.65	0.93	0.93	2	-
GCF_005938085.1	s__Natrinema sp005938085	89.7371	953	1138	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005576615.1	s__Natrinema versiforme_A	83.0481	755	1138	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002494345.1	s__Natrinema ejinorense	82.7039	743	1138	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_900110865.1	s__Natrinema salaciae	82.6862	778	1138	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:04,887] [INFO] GTDB search result was written to GCF_000337475.1_ASM33747v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:04,887] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:04,893] [INFO] DFAST_QC result json was written to GCF_000337475.1_ASM33747v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:04,894] [INFO] DFAST_QC completed!
[2024-01-25 20:19:04,894] [INFO] Total running time: 0h1m14s