[2024-01-24 13:46:03,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg196768cf-e240-4a56-b836-4af8e86eda58/dqc_reference
[2024-01-24 13:46:05,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:05,069] [INFO] Task started: Prodigal
[2024-01-24 13:46:05,070] [INFO] Running command: gunzip -c /var/lib/cwl/stg846b7adb-7017-471d-90e0-3806a3b31dfd/GCF_009663395.1_ASM966339v1_genomic.fna.gz | prodigal -d GCF_009663395.1_ASM966339v1_genomic.fna/cds.fna -a GCF_009663395.1_ASM966339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:20,193] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:20,194] [INFO] Task started: HMMsearch
[2024-01-24 13:46:20,194] [INFO] Running command: hmmsearch --tblout GCF_009663395.1_ASM966339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg196768cf-e240-4a56-b836-4af8e86eda58/dqc_reference/reference_markers.hmm GCF_009663395.1_ASM966339v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:20,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:20,405] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg846b7adb-7017-471d-90e0-3806a3b31dfd/GCF_009663395.1_ASM966339v1_genomic.fna.gz]
[2024-01-24 13:46:20,442] [INFO] Query marker FASTA was written to GCF_009663395.1_ASM966339v1_genomic.fna/markers.fasta
[2024-01-24 13:46:20,442] [INFO] Task started: Blastn
[2024-01-24 13:46:20,443] [INFO] Running command: blastn -query GCF_009663395.1_ASM966339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg196768cf-e240-4a56-b836-4af8e86eda58/dqc_reference/reference_markers.fasta -out GCF_009663395.1_ASM966339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:20,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:20,981] [INFO] Selected 9 target genomes.
[2024-01-24 13:46:20,982] [INFO] Target genome list was writen to GCF_009663395.1_ASM966339v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:20,988] [INFO] Task started: fastANI
[2024-01-24 13:46:20,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg846b7adb-7017-471d-90e0-3806a3b31dfd/GCF_009663395.1_ASM966339v1_genomic.fna.gz --refList GCF_009663395.1_ASM966339v1_genomic.fna/target_genomes.txt --output GCF_009663395.1_ASM966339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:28,141] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:28,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg196768cf-e240-4a56-b836-4af8e86eda58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:28,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg196768cf-e240-4a56-b836-4af8e86eda58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:28,150] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:28,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:28,151] [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
Halosegnis longus	strain=F12-1	GCA_009663395.1	2216012	2216012	type	True	100.0	921	922	95	conclusive
Halosegnis rubeus	strain=F17-44	GCA_009184545.1	2212850	2212850	type	True	91.507	701	922	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	78.4226	352	922	95	below_threshold
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	78.2322	337	922	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	78.1984	375	922	95	below_threshold
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	77.9372	307	922	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	77.6881	313	922	95	below_threshold
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	77.4687	322	922	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	77.4535	293	922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:28,152] [INFO] DFAST Taxonomy check result was written to GCF_009663395.1_ASM966339v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:28,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:28,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:28,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg196768cf-e240-4a56-b836-4af8e86eda58/dqc_reference/checkm_data
[2024-01-24 13:46:28,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:28,185] [INFO] Task started: CheckM
[2024-01-24 13:46:28,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009663395.1_ASM966339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009663395.1_ASM966339v1_genomic.fna/checkm_input GCF_009663395.1_ASM966339v1_genomic.fna/checkm_result
[2024-01-24 13:47:11,894] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:11,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:11,913] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:11,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:11,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009663395.1_ASM966339v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:11,914] [INFO] Task started: Blastn
[2024-01-24 13:47:11,914] [INFO] Running command: blastn -query GCF_009663395.1_ASM966339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg196768cf-e240-4a56-b836-4af8e86eda58/dqc_reference/reference_markers_gtdb.fasta -out GCF_009663395.1_ASM966339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:12,400] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:12,406] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:12,406] [INFO] Target genome list was writen to GCF_009663395.1_ASM966339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:12,418] [INFO] Task started: fastANI
[2024-01-24 13:47:12,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg846b7adb-7017-471d-90e0-3806a3b31dfd/GCF_009663395.1_ASM966339v1_genomic.fna.gz --refList GCF_009663395.1_ASM966339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009663395.1_ASM966339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:17,999] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:18,007] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:18,008] [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_001950595.1	s__CBA1134 sp001950595	99.2053	809	922	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	99.03	98.86	0.91	0.88	3	conclusive
GCF_009184545.1	s__CBA1134 sp009184545	91.507	701	922	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	99.60	99.56	0.94	0.94	3	-
GCA_003021785.1	s__CBA1134 sp003021785	84.2987	579	922	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	97.75	97.59	0.93	0.92	3	-
GCA_003021175.1	s__CBA1134 sp003021175	80.4185	461	922	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023185.1	s__CBA1134 sp003023185	80.2329	366	922	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	78.4121	353	922	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119205.1	s__Halomicroarcula limicola	77.7993	327	922	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004118325.1	s__Halorientalis sp004118325	77.4135	297	922	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839515.1	s__Natronomonas sp013839515	77.4076	224	922	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:18,009] [INFO] GTDB search result was written to GCF_009663395.1_ASM966339v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:18,010] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:18,013] [INFO] DFAST_QC result json was written to GCF_009663395.1_ASM966339v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:18,013] [INFO] DFAST_QC completed!
[2024-01-24 13:47:18,013] [INFO] Total running time: 0h1m14s