[2024-01-24 13:18:33,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,589] [INFO] DQC Reference Directory: /var/lib/cwl/stgf619ae8a-2f9d-4f92-bc57-6131f7921e11/dqc_reference
[2024-01-24 13:18:34,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,883] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a526cfd-992d-4e83-94c7-b707717d242e/GCF_000495475.1_Htyrrel1.0_genomic.fna.gz | prodigal -d GCF_000495475.1_Htyrrel1.0_genomic.fna/cds.fna -a GCF_000495475.1_Htyrrel1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:53,114] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:53,114] [INFO] Task started: HMMsearch
[2024-01-24 13:18:53,114] [INFO] Running command: hmmsearch --tblout GCF_000495475.1_Htyrrel1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf619ae8a-2f9d-4f92-bc57-6131f7921e11/dqc_reference/reference_markers.hmm GCF_000495475.1_Htyrrel1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:53,361] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:53,363] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7a526cfd-992d-4e83-94c7-b707717d242e/GCF_000495475.1_Htyrrel1.0_genomic.fna.gz]
[2024-01-24 13:18:53,405] [INFO] Query marker FASTA was written to GCF_000495475.1_Htyrrel1.0_genomic.fna/markers.fasta
[2024-01-24 13:18:53,405] [INFO] Task started: Blastn
[2024-01-24 13:18:53,405] [INFO] Running command: blastn -query GCF_000495475.1_Htyrrel1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgf619ae8a-2f9d-4f92-bc57-6131f7921e11/dqc_reference/reference_markers.fasta -out GCF_000495475.1_Htyrrel1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:54,027] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:54,030] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:54,030] [INFO] Target genome list was writen to GCF_000495475.1_Htyrrel1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:18:54,038] [INFO] Task started: fastANI
[2024-01-24 13:18:54,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a526cfd-992d-4e83-94c7-b707717d242e/GCF_000495475.1_Htyrrel1.0_genomic.fna.gz --refList GCF_000495475.1_Htyrrel1.0_genomic.fna/target_genomes.txt --output GCF_000495475.1_Htyrrel1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:04,132] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:04,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf619ae8a-2f9d-4f92-bc57-6131f7921e11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:04,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf619ae8a-2f9d-4f92-bc57-6131f7921e11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:04,144] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:04,145] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:04,145] [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
Halobaculum magnesiiphilum	strain=NBRC 109044	GCA_019823105.1	1017351	1017351	type	True	80.7485	621	1194	95	below_threshold
Halobaculum salinum	strain=NJ-3-1	GCA_013402875.1	2743089	2743089	type	True	80.7272	626	1194	95	below_threshold
Halobaculum roseum	strain=CGMCC 1.15501	GCA_019880245.1	2175149	2175149	type	True	80.7125	627	1194	95	below_threshold
Halobaculum halophilum	strain=Gai3-2	GCA_013401515.1	2743090	2743090	type	True	80.6551	653	1194	95	below_threshold
Halobaculum rubrum	strain=C46	GCA_019880225.1	2872158	2872158	type	True	80.4554	581	1194	95	below_threshold
Halobaculum saliterrae	strain=WSA2	GCA_009831625.1	2073113	2073113	type	True	80.4265	616	1194	95	below_threshold
Halobaculum gomorrense	strain=DSM 9297	GCA_900129775.1	43928	43928	type	True	80.2748	604	1194	95	below_threshold
Halobellus litoreus	strain=GX31	GCA_024464595.1	755310	755310	type	True	78.2035	423	1194	95	below_threshold
Halobellus ruber	strain=MBLA0160	GCA_014212355.1	2761102	2761102	type	True	78.0982	411	1194	95	below_threshold
Halobellus captivus	strain=ZY21	GCA_007655485.1	2592614	2592614	type	True	77.9125	352	1194	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	77.431	436	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:04,147] [INFO] DFAST Taxonomy check result was written to GCF_000495475.1_Htyrrel1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:19:04,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:04,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:04,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf619ae8a-2f9d-4f92-bc57-6131f7921e11/dqc_reference/checkm_data
[2024-01-24 13:19:04,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:04,206] [INFO] Task started: CheckM
[2024-01-24 13:19:04,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000495475.1_Htyrrel1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000495475.1_Htyrrel1.0_genomic.fna/checkm_input GCF_000495475.1_Htyrrel1.0_genomic.fna/checkm_result
[2024-01-24 13:19:52,984] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:52,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:53,009] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:53,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:53,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000495475.1_Htyrrel1.0_genomic.fna/markers.fasta)
[2024-01-24 13:19:53,011] [INFO] Task started: Blastn
[2024-01-24 13:19:53,011] [INFO] Running command: blastn -query GCF_000495475.1_Htyrrel1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgf619ae8a-2f9d-4f92-bc57-6131f7921e11/dqc_reference/reference_markers_gtdb.fasta -out GCF_000495475.1_Htyrrel1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:53,524] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:53,529] [INFO] Selected 8 target genomes.
[2024-01-24 13:19:53,529] [INFO] Target genome list was writen to GCF_000495475.1_Htyrrel1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:53,537] [INFO] Task started: fastANI
[2024-01-24 13:19:53,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a526cfd-992d-4e83-94c7-b707717d242e/GCF_000495475.1_Htyrrel1.0_genomic.fna.gz --refList GCF_000495475.1_Htyrrel1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000495475.1_Htyrrel1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:00,514] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:00,529] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:00,529] [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_000495475.1	s__Halobaculum tyrrellense	100.0	1192	1194	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003020945.1	s__Halobaculum sp003020945	80.7076	555	1194	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013401515.1	s__Halobaculum sp013401515	80.6859	650	1194	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013402875.1	s__Halobaculum sp013402875	80.6029	639	1194	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831625.1	s__Halobaculum sp009831625	80.3939	619	1194	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129775.1	s__Halobaculum gomorrense	80.3451	597	1194	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665935.1	s__Halobellus sp003665935	77.9412	398	1194	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655485.1	s__Halobellus captivus	77.9181	352	1194	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:00,531] [INFO] GTDB search result was written to GCF_000495475.1_Htyrrel1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:00,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:00,535] [INFO] DFAST_QC result json was written to GCF_000495475.1_Htyrrel1.0_genomic.fna/dqc_result.json
[2024-01-24 13:20:00,536] [INFO] DFAST_QC completed!
[2024-01-24 13:20:00,536] [INFO] Total running time: 0h1m27s