[2024-01-24 12:06:14,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,577] [INFO] DQC Reference Directory: /var/lib/cwl/stgc285be0d-4f48-480d-9665-cc02aa93438a/dqc_reference
[2024-01-24 12:06:15,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,999] [INFO] Task started: Prodigal
[2024-01-24 12:06:16,000] [INFO] Running command: gunzip -c /var/lib/cwl/stgac3ddba6-4696-4786-9174-81f24e6bc5a6/GCF_023973145.1_ASM2397314v1_genomic.fna.gz | prodigal -d GCF_023973145.1_ASM2397314v1_genomic.fna/cds.fna -a GCF_023973145.1_ASM2397314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:36,430] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:36,430] [INFO] Task started: HMMsearch
[2024-01-24 12:06:36,430] [INFO] Running command: hmmsearch --tblout GCF_023973145.1_ASM2397314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc285be0d-4f48-480d-9665-cc02aa93438a/dqc_reference/reference_markers.hmm GCF_023973145.1_ASM2397314v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:36,777] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:36,780] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgac3ddba6-4696-4786-9174-81f24e6bc5a6/GCF_023973145.1_ASM2397314v1_genomic.fna.gz]
[2024-01-24 12:06:36,817] [INFO] Query marker FASTA was written to GCF_023973145.1_ASM2397314v1_genomic.fna/markers.fasta
[2024-01-24 12:06:36,817] [INFO] Task started: Blastn
[2024-01-24 12:06:36,817] [INFO] Running command: blastn -query GCF_023973145.1_ASM2397314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc285be0d-4f48-480d-9665-cc02aa93438a/dqc_reference/reference_markers.fasta -out GCF_023973145.1_ASM2397314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:37,359] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:37,362] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:37,363] [INFO] Target genome list was writen to GCF_023973145.1_ASM2397314v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:37,373] [INFO] Task started: fastANI
[2024-01-24 12:06:37,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgac3ddba6-4696-4786-9174-81f24e6bc5a6/GCF_023973145.1_ASM2397314v1_genomic.fna.gz --refList GCF_023973145.1_ASM2397314v1_genomic.fna/target_genomes.txt --output GCF_023973145.1_ASM2397314v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:48,748] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:48,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc285be0d-4f48-480d-9665-cc02aa93438a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:48,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc285be0d-4f48-480d-9665-cc02aa93438a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:48,762] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:48,762] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:48,762] [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
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	78.8534	573	1278	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	78.5266	502	1278	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	78.4611	506	1278	95	below_threshold
Natronorubrum sulfidifaciens	strain=JCM 14089	GCA_000337735.1	388259	388259	type	True	78.4055	444	1278	95	below_threshold
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	78.3931	515	1278	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	78.3699	499	1278	95	below_threshold
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	78.3484	433	1278	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	78.3306	446	1278	95	below_threshold
Natrialba magadii	strain=ATCC 43099	GCA_000025625.1	13769	13769	type	True	78.322	482	1278	95	below_threshold
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	78.32	453	1278	95	below_threshold
Natronorubrum bangense	strain=JCM 10635	GCA_004799645.1	61858	61858	type	True	78.309	436	1278	95	below_threshold
Natrialba magadii	strain=MS-3	GCA_000337875.1	13769	13769	type	True	78.2859	476	1278	95	below_threshold
Haloterrigena hispanica	strain=DSM 18328	GCA_004217335.1	392421	392421	type	True	78.2575	452	1278	95	below_threshold
Natronorubrum bangense	strain=JCM 10635	GCA_000337715.1	61858	61858	type	True	78.2559	425	1278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:48,764] [INFO] DFAST Taxonomy check result was written to GCF_023973145.1_ASM2397314v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:48,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:48,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:48,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc285be0d-4f48-480d-9665-cc02aa93438a/dqc_reference/checkm_data
[2024-01-24 12:06:48,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:48,822] [INFO] Task started: CheckM
[2024-01-24 12:06:48,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023973145.1_ASM2397314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023973145.1_ASM2397314v1_genomic.fna/checkm_input GCF_023973145.1_ASM2397314v1_genomic.fna/checkm_result
[2024-01-24 12:07:44,675] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:44,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:44,708] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:44,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:44,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023973145.1_ASM2397314v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:44,709] [INFO] Task started: Blastn
[2024-01-24 12:07:44,709] [INFO] Running command: blastn -query GCF_023973145.1_ASM2397314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc285be0d-4f48-480d-9665-cc02aa93438a/dqc_reference/reference_markers_gtdb.fasta -out GCF_023973145.1_ASM2397314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:45,218] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:45,222] [INFO] Selected 12 target genomes.
[2024-01-24 12:07:45,222] [INFO] Target genome list was writen to GCF_023973145.1_ASM2397314v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:45,238] [INFO] Task started: fastANI
[2024-01-24 12:07:45,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgac3ddba6-4696-4786-9174-81f24e6bc5a6/GCF_023973145.1_ASM2397314v1_genomic.fna.gz --refList GCF_023973145.1_ASM2397314v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023973145.1_ASM2397314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:54,956] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:54,977] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:07:54,977] [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_017357105.1	s__Tc-Br11 sp017357105	81.0306	731	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001564275.1	s__Tc-Br11 sp001564275	79.6462	493	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	99.79	99.79	0.91	0.91	2	-
GCF_008122205.1	s__Natronococcus sp008122205	78.8585	569	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002494345.1	s__Natrinema ejinorense	78.5457	482	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCA_003559215.1	s__Natronococcus sp003559215	78.5438	487	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	99.83	99.81	0.98	0.98	4	-
GCF_900110865.1	s__Natrinema salaciae	78.4986	505	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337735.1	s__Natronorubrum sulfidifaciens	78.4185	444	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002572525.1	s__Natrinema sp002572525	78.3621	482	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008245225.1	s__Natrarchaeobius swarupiae	78.3443	498	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	96.49	96.49	0.86	0.86	2	-
GCF_004799645.1	s__Natronorubrum bangense	78.3089	431	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	97.90	95.84	0.96	0.96	3	-
GCF_000025625.1	s__Natrialba magadii	78.2754	485	1278	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004217335.1	s__Natrinema hispanicum	78.2662	449	1278	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 12:07:54,980] [INFO] GTDB search result was written to GCF_023973145.1_ASM2397314v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:54,980] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:54,984] [INFO] DFAST_QC result json was written to GCF_023973145.1_ASM2397314v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:54,984] [INFO] DFAST_QC completed!
[2024-01-24 12:07:54,984] [INFO] Total running time: 0h1m40s