[2024-01-24 15:06:36,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,579] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0b43981-1388-4813-a234-d4264f7a08b4/dqc_reference
[2024-01-24 15:06:38,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,060] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,060] [INFO] Running command: gunzip -c /var/lib/cwl/stgde6ca7a5-b1cb-4908-8441-96687b980441/GCF_013391105.1_ASM1339110v1_genomic.fna.gz | prodigal -d GCF_013391105.1_ASM1339110v1_genomic.fna/cds.fna -a GCF_013391105.1_ASM1339110v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:55,748] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:55,749] [INFO] Task started: HMMsearch
[2024-01-24 15:06:55,749] [INFO] Running command: hmmsearch --tblout GCF_013391105.1_ASM1339110v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0b43981-1388-4813-a234-d4264f7a08b4/dqc_reference/reference_markers.hmm GCF_013391105.1_ASM1339110v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:56,049] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:56,052] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgde6ca7a5-b1cb-4908-8441-96687b980441/GCF_013391105.1_ASM1339110v1_genomic.fna.gz]
[2024-01-24 15:06:56,108] [INFO] Query marker FASTA was written to GCF_013391105.1_ASM1339110v1_genomic.fna/markers.fasta
[2024-01-24 15:06:56,109] [INFO] Task started: Blastn
[2024-01-24 15:06:56,110] [INFO] Running command: blastn -query GCF_013391105.1_ASM1339110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0b43981-1388-4813-a234-d4264f7a08b4/dqc_reference/reference_markers.fasta -out GCF_013391105.1_ASM1339110v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:56,697] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:56,701] [INFO] Selected 9 target genomes.
[2024-01-24 15:06:56,701] [INFO] Target genome list was writen to GCF_013391105.1_ASM1339110v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:56,719] [INFO] Task started: fastANI
[2024-01-24 15:06:56,719] [INFO] Running command: fastANI --query /var/lib/cwl/stgde6ca7a5-b1cb-4908-8441-96687b980441/GCF_013391105.1_ASM1339110v1_genomic.fna.gz --refList GCF_013391105.1_ASM1339110v1_genomic.fna/target_genomes.txt --output GCF_013391105.1_ASM1339110v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:05,811] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:05,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0b43981-1388-4813-a234-d4264f7a08b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:05,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0b43981-1388-4813-a234-d4264f7a08b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:05,820] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:07:05,821] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:05,821] [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 salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	100.0	1248	1248	95	conclusive
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	81.4281	639	1248	95	below_threshold
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	81.2095	653	1248	95	below_threshold
Natronomonas moolapensis	strain=8.8.11	GCA_000591055.1	416273	416273	type	True	79.6563	445	1248	95	below_threshold
Natronomonas pharaonis	strain=Gabara	GCA_000026045.1	2257	2257	type	True	79.5989	422	1248	95	below_threshold
Natronomonas salsuginis	strain=F20-122	GCA_005239135.1	2217661	2217661	type	True	79.3831	446	1248	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	78.6968	523	1248	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	78.5275	516	1248	95	below_threshold
Halosimplex salinum	strain=YPL4	GCA_003730195.1	1710538	1710538	type	True	78.2751	522	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:05,822] [INFO] DFAST Taxonomy check result was written to GCF_013391105.1_ASM1339110v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:05,823] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:05,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:05,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0b43981-1388-4813-a234-d4264f7a08b4/dqc_reference/checkm_data
[2024-01-24 15:07:05,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:05,861] [INFO] Task started: CheckM
[2024-01-24 15:07:05,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013391105.1_ASM1339110v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013391105.1_ASM1339110v1_genomic.fna/checkm_input GCF_013391105.1_ASM1339110v1_genomic.fna/checkm_result
[2024-01-24 15:07:52,984] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:52,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:07:53,007] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:53,007] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:53,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013391105.1_ASM1339110v1_genomic.fna/markers.fasta)
[2024-01-24 15:07:53,008] [INFO] Task started: Blastn
[2024-01-24 15:07:53,009] [INFO] Running command: blastn -query GCF_013391105.1_ASM1339110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0b43981-1388-4813-a234-d4264f7a08b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013391105.1_ASM1339110v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:53,563] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:53,575] [INFO] Selected 12 target genomes.
[2024-01-24 15:07:53,576] [INFO] Target genome list was writen to GCF_013391105.1_ASM1339110v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:53,623] [INFO] Task started: fastANI
[2024-01-24 15:07:53,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgde6ca7a5-b1cb-4908-8441-96687b980441/GCF_013391105.1_ASM1339110v1_genomic.fna.gz --refList GCF_013391105.1_ASM1339110v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013391105.1_ASM1339110v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:08:02,267] [INFO] Task succeeded: fastANI
[2024-01-24 15:08:02,282] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:08:02,282] [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_013391105.1	s__Natronomonas salina	100.0	1248	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018609665.1	s__Natronomonas sp018609665	82.3373	476	1248	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	81.6558	657	1248	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	81.6517	619	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021325.1	s__Natronomonas sp003021325	81.6259	387	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020965.1	s__Natronomonas sp003020965	81.5486	603	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007135435.1	s__Natronomonas sp007135435	80.9342	432	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022905.1	s__Natronomonas sp003022905	80.9018	336	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021005.1	s__Natronomonas sp003021005	80.7639	490	1248	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	79.709	440	1248	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	79.3989	445	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122455.1	s__Natronomonas sp007122455	79.1689	377	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	99.45	99.45	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:08:02,284] [INFO] GTDB search result was written to GCF_013391105.1_ASM1339110v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:08:02,285] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:08:02,289] [INFO] DFAST_QC result json was written to GCF_013391105.1_ASM1339110v1_genomic.fna/dqc_result.json
[2024-01-24 15:08:02,289] [INFO] DFAST_QC completed!
[2024-01-24 15:08:02,289] [INFO] Total running time: 0h1m26s