[2024-01-24 14:04:31,886] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:04:31,888] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:04:31,889] [INFO] DQC Reference Directory: /var/lib/cwl/stga35cb7e4-ae5b-48ae-850c-33b8d8c52b7b/dqc_reference
[2024-01-24 14:04:33,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:04:33,249] [INFO] Task started: Prodigal
[2024-01-24 14:04:33,249] [INFO] Running command: gunzip -c /var/lib/cwl/stgb48914bd-4665-4ea0-bb2b-0cab21fb926a/GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/cds.fna -a GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:04:53,450] [INFO] Task succeeded: Prodigal
[2024-01-24 14:04:53,451] [INFO] Task started: HMMsearch
[2024-01-24 14:04:53,451] [INFO] Running command: hmmsearch --tblout GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga35cb7e4-ae5b-48ae-850c-33b8d8c52b7b/dqc_reference/reference_markers.hmm GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:04:53,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:04:53,748] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb48914bd-4665-4ea0-bb2b-0cab21fb926a/GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna.gz]
[2024-01-24 14:04:53,786] [INFO] Query marker FASTA was written to GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:04:53,787] [INFO] Task started: Blastn
[2024-01-24 14:04:53,787] [INFO] Running command: blastn -query GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga35cb7e4-ae5b-48ae-850c-33b8d8c52b7b/dqc_reference/reference_markers.fasta -out GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:54,333] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:54,339] [INFO] Selected 8 target genomes.
[2024-01-24 14:04:54,339] [INFO] Target genome list was writen to GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:04:54,374] [INFO] Task started: fastANI
[2024-01-24 14:04:54,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48914bd-4665-4ea0-bb2b-0cab21fb926a/GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna.gz --refList GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:02,728] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:02,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga35cb7e4-ae5b-48ae-850c-33b8d8c52b7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:02,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga35cb7e4-ae5b-48ae-850c-33b8d8c52b7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:02,742] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:02,743] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:02,743] [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
Halostagnicola kamekurae	strain=DSM 22427	GCA_900116205.1	619731	619731	type	True	100.0	1359	1360	95	conclusive
Halostagnicola larsenii	strain=XH-48	GCA_000517625.1	353800	353800	type	True	87.5301	961	1360	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	80.3405	619	1360	95	below_threshold
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	79.9098	599	1360	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	79.8827	625	1360	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.7833	603	1360	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	79.773	602	1360	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	79.7729	626	1360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:02,745] [INFO] DFAST Taxonomy check result was written to GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:05:02,745] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:02,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:02,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga35cb7e4-ae5b-48ae-850c-33b8d8c52b7b/dqc_reference/checkm_data
[2024-01-24 14:05:02,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:02,810] [INFO] Task started: CheckM
[2024-01-24 14:05:02,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/checkm_input GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:05:56,453] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:56,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:56,476] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:56,477] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:56,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:05:56,478] [INFO] Task started: Blastn
[2024-01-24 14:05:56,478] [INFO] Running command: blastn -query GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga35cb7e4-ae5b-48ae-850c-33b8d8c52b7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:56,963] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:56,967] [INFO] Selected 8 target genomes.
[2024-01-24 14:05:56,967] [INFO] Target genome list was writen to GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:57,016] [INFO] Task started: fastANI
[2024-01-24 14:05:57,016] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48914bd-4665-4ea0-bb2b-0cab21fb926a/GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna.gz --refList GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:05,015] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:05,024] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:05,024] [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_900116205.1	s__Halostagnicola kamekurae	100.0	1359	1360	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halostagnicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000691505.1	s__Halostagnicola sp000691505	92.0871	820	1360	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halostagnicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517625.1	s__Halostagnicola larsenii	87.5379	960	1360	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halostagnicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013456555.1	s__Natrinema sp013456555	79.9824	571	1360	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337695.1	s__Natronococcus jeotgali	79.9242	597	1360	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCF_002572525.1	s__Natrinema sp002572525	79.9129	638	1360	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	79.7973	602	1360	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_004217335.1	s__Natrinema hispanicum	79.4789	519	1360	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:05,032] [INFO] GTDB search result was written to GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:05,032] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:05,035] [INFO] DFAST_QC result json was written to GCF_900116205.1_IMG-taxon_2639762563_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:06:05,036] [INFO] DFAST_QC completed!
[2024-01-24 14:06:05,036] [INFO] Total running time: 0h1m33s