[2024-01-25 19:05:50,499] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:50,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:50,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgaced53c2-661c-4f56-a396-ac731a439148/dqc_reference
[2024-01-25 19:05:51,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:51,682] [INFO] Task started: Prodigal
[2024-01-25 19:05:51,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg44ffeae3-dfc8-496b-bb8f-26502947d3a7/GCF_017873815.1_ASM1787381v1_genomic.fna.gz | prodigal -d GCF_017873815.1_ASM1787381v1_genomic.fna/cds.fna -a GCF_017873815.1_ASM1787381v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:04,171] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:04,171] [INFO] Task started: HMMsearch
[2024-01-25 19:06:04,171] [INFO] Running command: hmmsearch --tblout GCF_017873815.1_ASM1787381v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaced53c2-661c-4f56-a396-ac731a439148/dqc_reference/reference_markers.hmm GCF_017873815.1_ASM1787381v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:04,415] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:04,416] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg44ffeae3-dfc8-496b-bb8f-26502947d3a7/GCF_017873815.1_ASM1787381v1_genomic.fna.gz]
[2024-01-25 19:06:04,445] [INFO] Query marker FASTA was written to GCF_017873815.1_ASM1787381v1_genomic.fna/markers.fasta
[2024-01-25 19:06:04,445] [INFO] Task started: Blastn
[2024-01-25 19:06:04,445] [INFO] Running command: blastn -query GCF_017873815.1_ASM1787381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaced53c2-661c-4f56-a396-ac731a439148/dqc_reference/reference_markers.fasta -out GCF_017873815.1_ASM1787381v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:04,942] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:04,944] [INFO] Selected 11 target genomes.
[2024-01-25 19:06:04,945] [INFO] Target genome list was writen to GCF_017873815.1_ASM1787381v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:04,950] [INFO] Task started: fastANI
[2024-01-25 19:06:04,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ffeae3-dfc8-496b-bb8f-26502947d3a7/GCF_017873815.1_ASM1787381v1_genomic.fna.gz --refList GCF_017873815.1_ASM1787381v1_genomic.fna/target_genomes.txt --output GCF_017873815.1_ASM1787381v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:13,649] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:13,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaced53c2-661c-4f56-a396-ac731a439148/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:13,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaced53c2-661c-4f56-a396-ac731a439148/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:13,659] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:06:13,659] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:06:13,659] [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
Halorubrum aquaticum	strain=CGMCC 1.6377	GCA_900113615.1	387340	387340	type	True	82.7735	602	999	95	below_threshold
Halorubrum halodurans	strain=Cb34	GCA_002252985.1	1383851	1383851	type	True	82.6324	568	999	95	below_threshold
Halorubrum cibi	strain=DSM 19504	GCA_900182635.1	413815	413815	type	True	82.5101	604	999	95	below_threshold
Halorubrum aethiopicum	strain=SAH-A6	GCA_001542905.1	1758255	1758255	type	True	82.4097	625	999	95	below_threshold
Halorubrum rubrum	strain=YC87	GCA_024494685.1	1126240	1126240	type	True	82.3821	614	999	95	below_threshold
Halorubrum depositum	strain=Y78	GCA_007671725.1	2583992	2583992	type	True	82.3363	593	999	95	below_threshold
Halorubrum saccharovorum	strain=DSM 1137	GCA_000337915.1	2248	2248	type	True	82.1322	581	999	95	below_threshold
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	82.0476	596	999	95	below_threshold
Halorubrum tebenquichense	strain=DSM 14210	GCA_000337415.1	119434	119434	type	True	81.9346	588	999	95	below_threshold
Halorubrum persicum	strain=C49	GCA_002727125.1	1383844	1383844	type	True	81.9094	573	999	95	below_threshold
Halorubrum ezzemoulense	strain=DSM 17463	GCA_000421805.1	337243	337243	type	True	81.8304	588	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:13,661] [INFO] DFAST Taxonomy check result was written to GCF_017873815.1_ASM1787381v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:13,662] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:13,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:13,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaced53c2-661c-4f56-a396-ac731a439148/dqc_reference/checkm_data
[2024-01-25 19:06:13,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:13,695] [INFO] Task started: CheckM
[2024-01-25 19:06:13,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873815.1_ASM1787381v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873815.1_ASM1787381v1_genomic.fna/checkm_input GCF_017873815.1_ASM1787381v1_genomic.fna/checkm_result
[2024-01-25 19:06:50,581] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:50,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:50,607] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:50,608] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:50,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873815.1_ASM1787381v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:50,608] [INFO] Task started: Blastn
[2024-01-25 19:06:50,608] [INFO] Running command: blastn -query GCF_017873815.1_ASM1787381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaced53c2-661c-4f56-a396-ac731a439148/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873815.1_ASM1787381v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:51,205] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:51,208] [INFO] Selected 13 target genomes.
[2024-01-25 19:06:51,208] [INFO] Target genome list was writen to GCF_017873815.1_ASM1787381v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:51,233] [INFO] Task started: fastANI
[2024-01-25 19:06:51,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ffeae3-dfc8-496b-bb8f-26502947d3a7/GCF_017873815.1_ASM1787381v1_genomic.fna.gz --refList GCF_017873815.1_ASM1787381v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873815.1_ASM1787381v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:01,957] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:01,965] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:01,966] [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_017873815.1	s__Halorubrum alkaliphilum	100.0	997	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900113615.1	s__Halorubrum aquaticum	82.824	599	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252985.1	s__Halorubrum halodurans	82.648	566	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182635.1	s__Halorubrum cibi	82.5013	603	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542905.1	s__Halorubrum aethiopicum	82.4994	618	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697845.1	s__Halorubrum sp003697845	82.3686	624	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671725.1	s__Halorubrum depositum	82.2957	595	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287355.1	s__Halorubrum sp003287355	82.2845	601	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337915.1	s__Halorubrum saccharovorum	82.1348	579	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336995.1	s__Halorubrum aidingense	81.9638	579	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727125.1	s__Halorubrum persicum	81.91	573	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337415.1	s__Halorubrum tebenquichense	81.859	595	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.2282	N/A	N/A	N/A	N/A	1	-
GCF_002114285.1	s__Halorubrum ezzemoulense	81.8074	588	999	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.69	98.29	0.85	0.81	17	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:01,967] [INFO] GTDB search result was written to GCF_017873815.1_ASM1787381v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:01,968] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:01,970] [INFO] DFAST_QC result json was written to GCF_017873815.1_ASM1787381v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:01,971] [INFO] DFAST_QC completed!
[2024-01-25 19:07:01,971] [INFO] Total running time: 0h1m11s