[2024-01-24 11:58:20,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a329d43-755d-413e-8840-09693c6b14b5/dqc_reference
[2024-01-24 11:58:21,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,498] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg21af8091-36d2-4170-ad04-20e1c52dfe08/GCF_024298905.1_ASM2429890v1_genomic.fna.gz | prodigal -d GCF_024298905.1_ASM2429890v1_genomic.fna/cds.fna -a GCF_024298905.1_ASM2429890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:40,308] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:40,308] [INFO] Task started: HMMsearch
[2024-01-24 11:58:40,308] [INFO] Running command: hmmsearch --tblout GCF_024298905.1_ASM2429890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a329d43-755d-413e-8840-09693c6b14b5/dqc_reference/reference_markers.hmm GCF_024298905.1_ASM2429890v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:40,549] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:40,551] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg21af8091-36d2-4170-ad04-20e1c52dfe08/GCF_024298905.1_ASM2429890v1_genomic.fna.gz]
[2024-01-24 11:58:40,590] [INFO] Query marker FASTA was written to GCF_024298905.1_ASM2429890v1_genomic.fna/markers.fasta
[2024-01-24 11:58:40,590] [INFO] Task started: Blastn
[2024-01-24 11:58:40,590] [INFO] Running command: blastn -query GCF_024298905.1_ASM2429890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a329d43-755d-413e-8840-09693c6b14b5/dqc_reference/reference_markers.fasta -out GCF_024298905.1_ASM2429890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:41,146] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:41,150] [INFO] Selected 12 target genomes.
[2024-01-24 11:58:41,150] [INFO] Target genome list was writen to GCF_024298905.1_ASM2429890v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:41,171] [INFO] Task started: fastANI
[2024-01-24 11:58:41,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg21af8091-36d2-4170-ad04-20e1c52dfe08/GCF_024298905.1_ASM2429890v1_genomic.fna.gz --refList GCF_024298905.1_ASM2429890v1_genomic.fna/target_genomes.txt --output GCF_024298905.1_ASM2429890v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:50,630] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:50,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a329d43-755d-413e-8840-09693c6b14b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:50,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a329d43-755d-413e-8840-09693c6b14b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:50,642] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:58:50,643] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:58:50,643] [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	82.5538	670	1331	95	below_threshold
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	81.2742	652	1331	95	below_threshold
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	81.0309	629	1331	95	below_threshold
Natronomonas moolapensis	strain=8.8.11	GCA_000591055.1	416273	416273	type	True	79.6495	462	1331	95	below_threshold
Natronomonas pharaonis	strain=Gabara	GCA_000026045.1	2257	2257	type	True	79.5529	426	1331	95	below_threshold
Natronomonas salsuginis	strain=F20-122	GCA_005239135.1	2217661	2217661	type	True	78.8591	431	1331	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	78.4752	497	1331	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	78.4368	504	1331	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	77.8593	422	1331	95	below_threshold
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	77.6444	430	1331	95	below_threshold
Salinigranum halophilum	strain=YJ-53	GCA_007004735.1	2565931	2565931	type	True	77.6429	399	1331	95	below_threshold
Salinigranum rubrum	strain=GX10	GCA_002906575.1	755307	755307	type	True	77.5386	429	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:50,644] [INFO] DFAST Taxonomy check result was written to GCF_024298905.1_ASM2429890v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:50,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:50,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:50,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a329d43-755d-413e-8840-09693c6b14b5/dqc_reference/checkm_data
[2024-01-24 11:58:50,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:50,689] [INFO] Task started: CheckM
[2024-01-24 11:58:50,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024298905.1_ASM2429890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024298905.1_ASM2429890v1_genomic.fna/checkm_input GCF_024298905.1_ASM2429890v1_genomic.fna/checkm_result
[2024-01-24 11:59:42,087] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:42,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:42,108] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:42,108] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:42,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024298905.1_ASM2429890v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:42,109] [INFO] Task started: Blastn
[2024-01-24 11:59:42,109] [INFO] Running command: blastn -query GCF_024298905.1_ASM2429890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a329d43-755d-413e-8840-09693c6b14b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_024298905.1_ASM2429890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:42,616] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:42,619] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:42,619] [INFO] Target genome list was writen to GCF_024298905.1_ASM2429890v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:42,631] [INFO] Task started: fastANI
[2024-01-24 11:59:42,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg21af8091-36d2-4170-ad04-20e1c52dfe08/GCF_024298905.1_ASM2429890v1_genomic.fna.gz --refList GCF_024298905.1_ASM2429890v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024298905.1_ASM2429890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:50,420] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:50,435] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:59:50,435] [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
GCA_003021325.1	s__Natronomonas sp003021325	84.4807	436	1331	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	84.2247	542	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022815.1	s__Natronomonas sp003022815	83.7309	375	1331	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	83.6128	668	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023535.1	s__Natronomonas sp003023535	83.124	447	1331	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022945.1	s__Natronomonas sp003022945	83.0439	582	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_013391105.1	s__Natronomonas salina	82.5389	672	1331	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	82.0499	552	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_013391635.1	s__Natronomonas gomsonensis	81.5313	658	1331	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	80.1125	377	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_005239135.1	s__Natronomonas salsuginis	78.8247	436	1331	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	78.5462	364	1331	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 11:59:50,437] [INFO] GTDB search result was written to GCF_024298905.1_ASM2429890v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:50,437] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:50,440] [INFO] DFAST_QC result json was written to GCF_024298905.1_ASM2429890v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:50,441] [INFO] DFAST_QC completed!
[2024-01-24 11:59:50,441] [INFO] Total running time: 0h1m30s