[2024-01-24 12:23:50,942] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,944] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,944] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f3263a0-e5c6-46a5-a411-4fa47f9801fc/dqc_reference
[2024-01-24 12:23:52,237] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,238] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,238] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b0a0622-3a64-4a79-92fd-b689ee3615f8/GCF_005239135.1_ASM523913v1_genomic.fna.gz | prodigal -d GCF_005239135.1_ASM523913v1_genomic.fna/cds.fna -a GCF_005239135.1_ASM523913v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:07,181] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:07,182] [INFO] Task started: HMMsearch
[2024-01-24 12:24:07,182] [INFO] Running command: hmmsearch --tblout GCF_005239135.1_ASM523913v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f3263a0-e5c6-46a5-a411-4fa47f9801fc/dqc_reference/reference_markers.hmm GCF_005239135.1_ASM523913v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:07,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:07,430] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2b0a0622-3a64-4a79-92fd-b689ee3615f8/GCF_005239135.1_ASM523913v1_genomic.fna.gz]
[2024-01-24 12:24:07,462] [INFO] Query marker FASTA was written to GCF_005239135.1_ASM523913v1_genomic.fna/markers.fasta
[2024-01-24 12:24:07,462] [INFO] Task started: Blastn
[2024-01-24 12:24:07,463] [INFO] Running command: blastn -query GCF_005239135.1_ASM523913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f3263a0-e5c6-46a5-a411-4fa47f9801fc/dqc_reference/reference_markers.fasta -out GCF_005239135.1_ASM523913v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:08,000] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:08,005] [INFO] Selected 10 target genomes.
[2024-01-24 12:24:08,006] [INFO] Target genome list was writen to GCF_005239135.1_ASM523913v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:08,011] [INFO] Task started: fastANI
[2024-01-24 12:24:08,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b0a0622-3a64-4a79-92fd-b689ee3615f8/GCF_005239135.1_ASM523913v1_genomic.fna.gz --refList GCF_005239135.1_ASM523913v1_genomic.fna/target_genomes.txt --output GCF_005239135.1_ASM523913v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:15,162] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:15,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f3263a0-e5c6-46a5-a411-4fa47f9801fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:15,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f3263a0-e5c6-46a5-a411-4fa47f9801fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:15,175] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:15,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:15,176] [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 salsuginis	strain=F20-122	GCA_005239135.1	2217661	2217661	type	True	100.0	961	962	95	conclusive
Natronomonas moolapensis	strain=8.8.11	GCA_000591055.1	416273	416273	type	True	81.2867	504	962	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	79.3043	451	962	95	below_threshold
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	79.1014	429	962	95	below_threshold
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	78.7555	379	962	95	below_threshold
Natronomonas pharaonis	strain=Gabara	GCA_000026045.1	2257	2257	type	True	78.7013	350	962	95	below_threshold
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	77.8636	289	962	95	below_threshold
Halobaculum saliterrae	strain=WSA2	GCA_009831625.1	2073113	2073113	type	True	77.442	307	962	95	below_threshold
Natrinema gari	strain=JCM 14663	GCA_000337175.1	419186	419186	type	True	77.1971	243	962	95	below_threshold
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	77.1093	267	962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:15,178] [INFO] DFAST Taxonomy check result was written to GCF_005239135.1_ASM523913v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:15,178] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:15,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:15,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f3263a0-e5c6-46a5-a411-4fa47f9801fc/dqc_reference/checkm_data
[2024-01-24 12:24:15,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:15,210] [INFO] Task started: CheckM
[2024-01-24 12:24:15,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005239135.1_ASM523913v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005239135.1_ASM523913v1_genomic.fna/checkm_input GCF_005239135.1_ASM523913v1_genomic.fna/checkm_result
[2024-01-24 12:24:58,524] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:58,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:58,548] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:58,549] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:58,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005239135.1_ASM523913v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:58,550] [INFO] Task started: Blastn
[2024-01-24 12:24:58,550] [INFO] Running command: blastn -query GCF_005239135.1_ASM523913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f3263a0-e5c6-46a5-a411-4fa47f9801fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_005239135.1_ASM523913v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:59,072] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:59,076] [INFO] Selected 11 target genomes.
[2024-01-24 12:24:59,077] [INFO] Target genome list was writen to GCF_005239135.1_ASM523913v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:59,086] [INFO] Task started: fastANI
[2024-01-24 12:24:59,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b0a0622-3a64-4a79-92fd-b689ee3615f8/GCF_005239135.1_ASM523913v1_genomic.fna.gz --refList GCF_005239135.1_ASM523913v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005239135.1_ASM523913v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:06,723] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:06,743] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:06,744] [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_005239135.1	s__Natronomonas salsuginis	100.0	961	962	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_000591055.1	s__Natronomonas moolapensis	81.3287	501	962	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839515.1	s__Natronomonas sp013839515	81.2322	490	962	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	79.3017	452	962	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	79.0553	436	962	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	79.0521	418	962	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	77.8696	234	962	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831625.1	s__Halobaculum sp009831625	77.4105	311	962	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337175.1	s__Natrinema gari	77.1746	246	962	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.50	98.45	0.93	0.92	3	-
GCF_000337615.1	s__Natrinema pallidum	77.0696	272	962	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.94	98.94	0.86	0.86	2	-
GCF_003841505.1	s__Natrarchaeobius chitinivorans	76.8209	243	962	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:06,746] [INFO] GTDB search result was written to GCF_005239135.1_ASM523913v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:06,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:06,753] [INFO] DFAST_QC result json was written to GCF_005239135.1_ASM523913v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:06,753] [INFO] DFAST_QC completed!
[2024-01-24 12:25:06,753] [INFO] Total running time: 0h1m16s