[2024-01-24 12:31:03,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,131] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c0629ee-a447-4fc0-a5a3-7e1fe5399639/dqc_reference
[2024-01-24 12:31:04,358] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:04,358] [INFO] Task started: Prodigal
[2024-01-24 12:31:04,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d36a259-0ccd-471c-8e41-bc656e5d36e5/GCF_000026045.1_ASM2604v1_genomic.fna.gz | prodigal -d GCF_000026045.1_ASM2604v1_genomic.fna/cds.fna -a GCF_000026045.1_ASM2604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:16,780] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:16,780] [INFO] Task started: HMMsearch
[2024-01-24 12:31:16,780] [INFO] Running command: hmmsearch --tblout GCF_000026045.1_ASM2604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c0629ee-a447-4fc0-a5a3-7e1fe5399639/dqc_reference/reference_markers.hmm GCF_000026045.1_ASM2604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:16,995] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:16,996] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1d36a259-0ccd-471c-8e41-bc656e5d36e5/GCF_000026045.1_ASM2604v1_genomic.fna.gz]
[2024-01-24 12:31:17,018] [INFO] Query marker FASTA was written to GCF_000026045.1_ASM2604v1_genomic.fna/markers.fasta
[2024-01-24 12:31:17,018] [INFO] Task started: Blastn
[2024-01-24 12:31:17,019] [INFO] Running command: blastn -query GCF_000026045.1_ASM2604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0629ee-a447-4fc0-a5a3-7e1fe5399639/dqc_reference/reference_markers.fasta -out GCF_000026045.1_ASM2604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:17,520] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:17,525] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:17,525] [INFO] Target genome list was writen to GCF_000026045.1_ASM2604v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:17,532] [INFO] Task started: fastANI
[2024-01-24 12:31:17,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d36a259-0ccd-471c-8e41-bc656e5d36e5/GCF_000026045.1_ASM2604v1_genomic.fna.gz --refList GCF_000026045.1_ASM2604v1_genomic.fna/target_genomes.txt --output GCF_000026045.1_ASM2604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:24,026] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:24,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c0629ee-a447-4fc0-a5a3-7e1fe5399639/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:24,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c0629ee-a447-4fc0-a5a3-7e1fe5399639/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:24,033] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:24,033] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:24,034] [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
Natronomonas pharaonis	strain=Gabara	GCA_000026045.1	2257	2257	type	True	100.0	912	915	95	conclusive
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	79.6412	426	915	95	below_threshold
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	79.5393	430	915	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	79.5184	439	915	95	below_threshold
Natronomonas moolapensis	strain=8.8.11	GCA_000591055.1	416273	416273	type	True	78.8849	378	915	95	below_threshold
Natronomonas salsuginis	strain=F20-122	GCA_005239135.1	2217661	2217661	type	True	78.8209	341	915	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000336655.1	229731	229731	type	True	77.3253	220	915	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	77.3075	227	915	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	77.0365	215	915	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	76.9733	213	915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:24,035] [INFO] DFAST Taxonomy check result was written to GCF_000026045.1_ASM2604v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:24,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:24,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:24,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c0629ee-a447-4fc0-a5a3-7e1fe5399639/dqc_reference/checkm_data
[2024-01-24 12:31:24,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:24,065] [INFO] Task started: CheckM
[2024-01-24 12:31:24,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000026045.1_ASM2604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000026045.1_ASM2604v1_genomic.fna/checkm_input GCF_000026045.1_ASM2604v1_genomic.fna/checkm_result
[2024-01-24 12:31:59,529] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:59,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:59,547] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:59,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:59,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000026045.1_ASM2604v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:59,548] [INFO] Task started: Blastn
[2024-01-24 12:31:59,548] [INFO] Running command: blastn -query GCF_000026045.1_ASM2604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0629ee-a447-4fc0-a5a3-7e1fe5399639/dqc_reference/reference_markers_gtdb.fasta -out GCF_000026045.1_ASM2604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:00,038] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:00,042] [INFO] Selected 12 target genomes.
[2024-01-24 12:32:00,042] [INFO] Target genome list was writen to GCF_000026045.1_ASM2604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:00,048] [INFO] Task started: fastANI
[2024-01-24 12:32:00,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d36a259-0ccd-471c-8e41-bc656e5d36e5/GCF_000026045.1_ASM2604v1_genomic.fna.gz --refList GCF_000026045.1_ASM2604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000026045.1_ASM2604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:07,788] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:07,796] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:07,796] [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_000026045.1	s__Natronomonas pharaonis	100.0	913	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013391085.1	s__Natronomonas halophila	79.614	428	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741925.1	s__Natronomonas sp009741925	79.5598	409	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	79.543	436	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391635.1	s__Natronomonas gomsonensis	79.3147	436	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000591055.1	s__Natronomonas moolapensis	78.8952	376	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239135.1	s__Natronomonas salsuginis	78.859	338	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018609665.1	s__Natronomonas sp018609665	78.6863	320	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	77.3201	226	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_004217335.1	s__Natrinema hispanicum	77.1633	201	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110455.1	s__Natrinema salifodinae	77.0452	214	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_900116205.1	s__Halostagnicola kamekurae	76.5379	204	915	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halostagnicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:07,798] [INFO] GTDB search result was written to GCF_000026045.1_ASM2604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:07,799] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:07,802] [INFO] DFAST_QC result json was written to GCF_000026045.1_ASM2604v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:07,802] [INFO] DFAST_QC completed!
[2024-01-24 12:32:07,802] [INFO] Total running time: 0h1m5s