[2024-01-24 13:31:33,299] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,301] [INFO] DQC Reference Directory: /var/lib/cwl/stgc91ebcdf-bb8d-477f-9c50-c32e53ec7ebe/dqc_reference
[2024-01-24 13:31:34,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,650] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,650] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9c68bbc-2c23-44b4-b820-7ec17e69623a/GCF_009791395.1_ASM979139v1_genomic.fna.gz | prodigal -d GCF_009791395.1_ASM979139v1_genomic.fna/cds.fna -a GCF_009791395.1_ASM979139v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:56,406] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:56,406] [INFO] Task started: HMMsearch
[2024-01-24 13:31:56,406] [INFO] Running command: hmmsearch --tblout GCF_009791395.1_ASM979139v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc91ebcdf-bb8d-477f-9c50-c32e53ec7ebe/dqc_reference/reference_markers.hmm GCF_009791395.1_ASM979139v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:56,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:56,675] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc9c68bbc-2c23-44b4-b820-7ec17e69623a/GCF_009791395.1_ASM979139v1_genomic.fna.gz]
[2024-01-24 13:31:56,717] [INFO] Query marker FASTA was written to GCF_009791395.1_ASM979139v1_genomic.fna/markers.fasta
[2024-01-24 13:31:56,718] [INFO] Task started: Blastn
[2024-01-24 13:31:56,718] [INFO] Running command: blastn -query GCF_009791395.1_ASM979139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc91ebcdf-bb8d-477f-9c50-c32e53ec7ebe/dqc_reference/reference_markers.fasta -out GCF_009791395.1_ASM979139v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:57,240] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:57,245] [INFO] Selected 8 target genomes.
[2024-01-24 13:31:57,246] [INFO] Target genome list was writen to GCF_009791395.1_ASM979139v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:57,251] [INFO] Task started: fastANI
[2024-01-24 13:31:57,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c68bbc-2c23-44b4-b820-7ec17e69623a/GCF_009791395.1_ASM979139v1_genomic.fna.gz --refList GCF_009791395.1_ASM979139v1_genomic.fna/target_genomes.txt --output GCF_009791395.1_ASM979139v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:05,346] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:05,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc91ebcdf-bb8d-477f-9c50-c32e53ec7ebe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:05,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc91ebcdf-bb8d-477f-9c50-c32e53ec7ebe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:05,361] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:05,361] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:05,362] [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
Halomarina oriensis	strain=JCM 16495	GCA_009791395.1	671145	671145	type	True	100.0	1328	1331	95	conclusive
Halomarina rubra	strain=ZS-47-S	GCA_023699475.1	2071873	2071873	type	True	86.1796	913	1331	95	below_threshold
Halomarina salina	strain=ZS-57-S	GCA_023074835.1	1872699	1872699	type	True	84.8635	887	1331	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	78.2615	458	1331	95	below_threshold
Halomicrobium zhouii	strain=CGMCC 1.10457	GCA_900114435.1	767519	767519	type	True	77.8852	417	1331	95	below_threshold
Halorussus marinus	strain=LYG-36	GCA_004765795.1	2505976	2505976	type	True	77.756	410	1331	95	below_threshold
Haloplanus salinus	strain=JCM 18368	GCA_003336245.1	1126245	1126245	type	True	77.376	341	1331	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	76.9182	362	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:05,363] [INFO] DFAST Taxonomy check result was written to GCF_009791395.1_ASM979139v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:05,364] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:05,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:05,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc91ebcdf-bb8d-477f-9c50-c32e53ec7ebe/dqc_reference/checkm_data
[2024-01-24 13:32:05,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:05,412] [INFO] Task started: CheckM
[2024-01-24 13:32:05,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009791395.1_ASM979139v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009791395.1_ASM979139v1_genomic.fna/checkm_input GCF_009791395.1_ASM979139v1_genomic.fna/checkm_result
[2024-01-24 13:33:02,003] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:02,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:02,027] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:02,027] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:02,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009791395.1_ASM979139v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:02,028] [INFO] Task started: Blastn
[2024-01-24 13:33:02,028] [INFO] Running command: blastn -query GCF_009791395.1_ASM979139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc91ebcdf-bb8d-477f-9c50-c32e53ec7ebe/dqc_reference/reference_markers_gtdb.fasta -out GCF_009791395.1_ASM979139v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:02,531] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:02,536] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:02,537] [INFO] Target genome list was writen to GCF_009791395.1_ASM979139v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:02,547] [INFO] Task started: fastANI
[2024-01-24 13:33:02,548] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c68bbc-2c23-44b4-b820-7ec17e69623a/GCF_009791395.1_ASM979139v1_genomic.fna.gz --refList GCF_009791395.1_ASM979139v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009791395.1_ASM979139v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:12,641] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:12,651] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:12,651] [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_009791395.1	s__Halomarina oriensis	100.0	1328	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003021975.1	s__Halomarina sp003021975	79.4755	467	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	78.2609	457	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785955.1	s__Halostella litorea	78.1045	445	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114435.1	s__Halomicrobium zhouii	77.9046	414	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369835.1	s__Halorussus rarus	77.8004	477	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018609665.1	s__Natronomonas sp018609665	77.7127	320	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765795.1	s__Halorussus sp004765795	77.7113	415	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	98.88	98.88	0.88	0.88	2	-
GCF_003342675.1	s__Haloplanus rubicundus	77.6808	383	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	98.71	98.71	0.88	0.88	2	-
GCA_003020965.1	s__Natronomonas sp003020965	77.515	371	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336245.1	s__Haloplanus salinus	77.3789	340	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:12,653] [INFO] GTDB search result was written to GCF_009791395.1_ASM979139v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:12,653] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:12,656] [INFO] DFAST_QC result json was written to GCF_009791395.1_ASM979139v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:12,656] [INFO] DFAST_QC completed!
[2024-01-24 13:33:12,656] [INFO] Total running time: 0h1m39s