[2024-01-24 10:47:11,674] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg7870b0ee-5591-42b1-9125-b649c737e738/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stgcca6ba55-129b-479f-a351-77e1ac3f8c10/GCF_019880245.1_ASM1988024v1_genomic.fna.gz | prodigal -d GCF_019880245.1_ASM1988024v1_genomic.fna/cds.fna -a GCF_019880245.1_ASM1988024v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:37,289] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:37,289] [INFO] Task started: HMMsearch
[2024-01-24 10:47:37,289] [INFO] Running command: hmmsearch --tblout GCF_019880245.1_ASM1988024v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7870b0ee-5591-42b1-9125-b649c737e738/dqc_reference/reference_markers.hmm GCF_019880245.1_ASM1988024v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:37,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:37,559] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcca6ba55-129b-479f-a351-77e1ac3f8c10/GCF_019880245.1_ASM1988024v1_genomic.fna.gz]
[2024-01-24 10:47:37,594] [INFO] Query marker FASTA was written to GCF_019880245.1_ASM1988024v1_genomic.fna/markers.fasta
[2024-01-24 10:47:37,594] [INFO] Task started: Blastn
[2024-01-24 10:47:37,594] [INFO] Running command: blastn -query GCF_019880245.1_ASM1988024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7870b0ee-5591-42b1-9125-b649c737e738/dqc_reference/reference_markers.fasta -out GCF_019880245.1_ASM1988024v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:38,114] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:38,118] [INFO] Selected 5 target genomes.
[2024-01-24 10:47:38,118] [INFO] Target genome list was writen to GCF_019880245.1_ASM1988024v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:38,608] [INFO] Task started: fastANI
[2024-01-24 10:47:38,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgcca6ba55-129b-479f-a351-77e1ac3f8c10/GCF_019880245.1_ASM1988024v1_genomic.fna.gz --refList GCF_019880245.1_ASM1988024v1_genomic.fna/target_genomes.txt --output GCF_019880245.1_ASM1988024v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:44,451] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:44,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7870b0ee-5591-42b1-9125-b649c737e738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:44,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7870b0ee-5591-42b1-9125-b649c737e738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:44,459] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:44,459] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:47:44,459] [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 roseum	strain=CGMCC 1.15501	GCA_019880245.1	2175149	2175149	type	True	100.0	1238	1238	95	inconclusive
Halobaculum magnesiiphilum	strain=NBRC 109044	GCA_019823105.1	1017351	1017351	type	True	95.4089	1034	1238	95	inconclusive
Halobaculum rubrum	strain=C46	GCA_019880225.1	2872158	2872158	type	True	88.5589	838	1238	95	below_threshold
Halobaculum saliterrae	strain=WSA2	GCA_009831625.1	2073113	2073113	type	True	88.4866	950	1238	95	below_threshold
Halobaculum gomorrense	strain=DSM 9297	GCA_900129775.1	43928	43928	type	True	87.7541	813	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:44,461] [INFO] DFAST Taxonomy check result was written to GCF_019880245.1_ASM1988024v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:44,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:44,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:44,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7870b0ee-5591-42b1-9125-b649c737e738/dqc_reference/checkm_data
[2024-01-24 10:47:44,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:44,504] [INFO] Task started: CheckM
[2024-01-24 10:47:44,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019880245.1_ASM1988024v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019880245.1_ASM1988024v1_genomic.fna/checkm_input GCF_019880245.1_ASM1988024v1_genomic.fna/checkm_result
[2024-01-24 10:48:34,129] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:34,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,161] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:34,161] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:34,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019880245.1_ASM1988024v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:34,162] [INFO] Task started: Blastn
[2024-01-24 10:48:34,162] [INFO] Running command: blastn -query GCF_019880245.1_ASM1988024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7870b0ee-5591-42b1-9125-b649c737e738/dqc_reference/reference_markers_gtdb.fasta -out GCF_019880245.1_ASM1988024v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:34,729] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:34,733] [INFO] Selected 7 target genomes.
[2024-01-24 10:48:34,734] [INFO] Target genome list was writen to GCF_019880245.1_ASM1988024v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:34,758] [INFO] Task started: fastANI
[2024-01-24 10:48:34,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgcca6ba55-129b-479f-a351-77e1ac3f8c10/GCF_019880245.1_ASM1988024v1_genomic.fna.gz --refList GCF_019880245.1_ASM1988024v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019880245.1_ASM1988024v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:41,490] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:41,501] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:41,501] [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_009831625.1	s__Halobaculum sp009831625	88.4866	950	1238	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	87.8032	810	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020945.1	s__Halobaculum sp003020945	84.985	679	1238	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	81.3143	678	1238	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	81.2234	681	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495475.1	s__Halobaculum tyrrellense	80.6482	633	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990725.2	s__Halorubrum sp003990725	78.4021	453	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.05	98.05	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:41,503] [INFO] GTDB search result was written to GCF_019880245.1_ASM1988024v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:41,503] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:41,506] [INFO] DFAST_QC result json was written to GCF_019880245.1_ASM1988024v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:41,506] [INFO] DFAST_QC completed!
[2024-01-24 10:48:41,506] [INFO] Total running time: 0h1m30s