[2024-01-24 11:21:07,410] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,411] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg68860e45-145c-49b5-bd59-7f8632666b61/dqc_reference
[2024-01-24 11:21:11,959] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,960] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,960] [INFO] Running command: gunzip -c /var/lib/cwl/stga4362478-1293-4e7a-851a-25d991939dea/GCF_026712385.1_ASM2671238v1_genomic.fna.gz | prodigal -d GCF_026712385.1_ASM2671238v1_genomic.fna/cds.fna -a GCF_026712385.1_ASM2671238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:32,638] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:32,638] [INFO] Task started: HMMsearch
[2024-01-24 11:21:32,638] [INFO] Running command: hmmsearch --tblout GCF_026712385.1_ASM2671238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68860e45-145c-49b5-bd59-7f8632666b61/dqc_reference/reference_markers.hmm GCF_026712385.1_ASM2671238v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:32,898] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:32,899] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga4362478-1293-4e7a-851a-25d991939dea/GCF_026712385.1_ASM2671238v1_genomic.fna.gz]
[2024-01-24 11:21:32,936] [INFO] Query marker FASTA was written to GCF_026712385.1_ASM2671238v1_genomic.fna/markers.fasta
[2024-01-24 11:21:32,936] [INFO] Task started: Blastn
[2024-01-24 11:21:32,937] [INFO] Running command: blastn -query GCF_026712385.1_ASM2671238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68860e45-145c-49b5-bd59-7f8632666b61/dqc_reference/reference_markers.fasta -out GCF_026712385.1_ASM2671238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:33,451] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:33,455] [INFO] Selected 8 target genomes.
[2024-01-24 11:21:33,456] [INFO] Target genome list was writen to GCF_026712385.1_ASM2671238v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:33,460] [INFO] Task started: fastANI
[2024-01-24 11:21:33,461] [INFO] Running command: fastANI --query /var/lib/cwl/stga4362478-1293-4e7a-851a-25d991939dea/GCF_026712385.1_ASM2671238v1_genomic.fna.gz --refList GCF_026712385.1_ASM2671238v1_genomic.fna/target_genomes.txt --output GCF_026712385.1_ASM2671238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:39,540] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:39,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68860e45-145c-49b5-bd59-7f8632666b61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:39,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68860e45-145c-49b5-bd59-7f8632666b61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:39,548] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:39,549] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:39,549] [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 gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	99.9495	1161	1304	95	conclusive
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	81.5481	644	1304	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	81.1149	658	1304	95	below_threshold
Natronomonas pharaonis	strain=Gabara	GCA_000026045.1	2257	2257	type	True	79.4632	438	1304	95	below_threshold
Natronomonas moolapensis	strain=8.8.11	GCA_000591055.1	416273	416273	type	True	79.3362	438	1304	95	below_threshold
Natronomonas salsuginis	strain=F20-122	GCA_005239135.1	2217661	2217661	type	True	78.9436	417	1304	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	77.5809	383	1304	95	below_threshold
Natronoarchaeum rubrum	strain=GX48	GCA_024494695.1	755311	755311	type	True	77.3654	332	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:39,553] [INFO] DFAST Taxonomy check result was written to GCF_026712385.1_ASM2671238v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:39,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:39,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:39,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68860e45-145c-49b5-bd59-7f8632666b61/dqc_reference/checkm_data
[2024-01-24 11:21:39,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:39,596] [INFO] Task started: CheckM
[2024-01-24 11:21:39,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026712385.1_ASM2671238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026712385.1_ASM2671238v1_genomic.fna/checkm_input GCF_026712385.1_ASM2671238v1_genomic.fna/checkm_result
[2024-01-24 11:22:35,924] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:35,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:35,942] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:35,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:35,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026712385.1_ASM2671238v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:35,943] [INFO] Task started: Blastn
[2024-01-24 11:22:35,943] [INFO] Running command: blastn -query GCF_026712385.1_ASM2671238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68860e45-145c-49b5-bd59-7f8632666b61/dqc_reference/reference_markers_gtdb.fasta -out GCF_026712385.1_ASM2671238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:36,420] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:36,423] [INFO] Selected 9 target genomes.
[2024-01-24 11:22:36,423] [INFO] Target genome list was writen to GCF_026712385.1_ASM2671238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:36,429] [INFO] Task started: fastANI
[2024-01-24 11:22:36,429] [INFO] Running command: fastANI --query /var/lib/cwl/stga4362478-1293-4e7a-851a-25d991939dea/GCF_026712385.1_ASM2671238v1_genomic.fna.gz --refList GCF_026712385.1_ASM2671238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026712385.1_ASM2671238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:42,994] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:43,009] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:22:43,010] [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_009741925.1	s__Natronomonas sp009741925	93.1955	879	1304	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	92.6041	887	1304	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391085.1	s__Natronomonas halophila	81.5589	642	1304	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	81.0796	663	1304	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	80.0741	518	1304	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	79.8866	336	1304	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	78.9654	386	1304	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	78.3477	328	1304	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	99.45	99.45	0.87	0.87	2	-
GCF_004118325.1	s__Halorientalis sp004118325	77.6052	381	1304	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:43,011] [INFO] GTDB search result was written to GCF_026712385.1_ASM2671238v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:43,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:43,014] [INFO] DFAST_QC result json was written to GCF_026712385.1_ASM2671238v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:43,015] [INFO] DFAST_QC completed!
[2024-01-24 11:22:43,015] [INFO] Total running time: 0h1m36s