[2023-06-17 11:08:15,347] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:08:15,350] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:08:15,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f8f432c-6473-437c-b8c3-0ca9ae9ba4e0/dqc_reference
[2023-06-17 11:08:16,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:08:16,907] [INFO] Task started: Prodigal
[2023-06-17 11:08:16,907] [INFO] Running command: gunzip -c /var/lib/cwl/stgdca96a43-dd00-4433-91fc-b266114c03df/GCA_003020945.1_ASM302094v1_genomic.fna.gz | prodigal -d GCA_003020945.1_ASM302094v1_genomic.fna/cds.fna -a GCA_003020945.1_ASM302094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:08:28,923] [INFO] Task succeeded: Prodigal
[2023-06-17 11:08:28,924] [INFO] Task started: HMMsearch
[2023-06-17 11:08:28,924] [INFO] Running command: hmmsearch --tblout GCA_003020945.1_ASM302094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f8f432c-6473-437c-b8c3-0ca9ae9ba4e0/dqc_reference/reference_markers.hmm GCA_003020945.1_ASM302094v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:08:29,141] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:08:29,142] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgdca96a43-dd00-4433-91fc-b266114c03df/GCA_003020945.1_ASM302094v1_genomic.fna.gz]
[2023-06-17 11:08:29,171] [INFO] Query marker FASTA was written to GCA_003020945.1_ASM302094v1_genomic.fna/markers.fasta
[2023-06-17 11:08:29,171] [INFO] Task started: Blastn
[2023-06-17 11:08:29,171] [INFO] Running command: blastn -query GCA_003020945.1_ASM302094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f8f432c-6473-437c-b8c3-0ca9ae9ba4e0/dqc_reference/reference_markers.fasta -out GCA_003020945.1_ASM302094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:08:29,730] [INFO] Task succeeded: Blastn
[2023-06-17 11:08:29,734] [INFO] Selected 6 target genomes.
[2023-06-17 11:08:29,734] [INFO] Target genome list was writen to GCA_003020945.1_ASM302094v1_genomic.fna/target_genomes.txt
[2023-06-17 11:08:29,738] [INFO] Task started: fastANI
[2023-06-17 11:08:29,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca96a43-dd00-4433-91fc-b266114c03df/GCA_003020945.1_ASM302094v1_genomic.fna.gz --refList GCA_003020945.1_ASM302094v1_genomic.fna/target_genomes.txt --output GCA_003020945.1_ASM302094v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:08:35,359] [INFO] Task succeeded: fastANI
[2023-06-17 11:08:35,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f8f432c-6473-437c-b8c3-0ca9ae9ba4e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:08:35,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f8f432c-6473-437c-b8c3-0ca9ae9ba4e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:08:35,367] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:08:35,367] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:08:35,368] [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	85.077	678	868	95	below_threshold
Halobaculum saliterrae	strain=WSA2	GCA_009831625.1	2073113	2073113	type	True	84.8328	682	868	95	below_threshold
Halobaculum magnesiiphilum	strain=NBRC 109044	GCA_019823105.1	1017351	1017351	type	True	84.8148	704	868	95	below_threshold
Halobaculum rubrum	strain=C46	GCA_019880225.1	2872158	2872158	type	True	84.6379	652	868	95	below_threshold
Halobaculum gomorrense	strain=DSM 9297	GCA_900129775.1	43928	43928	type	True	84.0606	663	868	95	below_threshold
Halobaculum halophilum	strain=Gai3-2	GCA_013401515.1	2743090	2743090	type	True	80.8725	572	868	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:08:35,370] [INFO] DFAST Taxonomy check result was written to GCA_003020945.1_ASM302094v1_genomic.fna/tc_result.tsv
[2023-06-17 11:08:35,371] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:08:35,371] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:08:35,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f8f432c-6473-437c-b8c3-0ca9ae9ba4e0/dqc_reference/checkm_data
[2023-06-17 11:08:35,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:08:35,405] [INFO] Task started: CheckM
[2023-06-17 11:08:35,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003020945.1_ASM302094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003020945.1_ASM302094v1_genomic.fna/checkm_input GCA_003020945.1_ASM302094v1_genomic.fna/checkm_result
[2023-06-17 11:09:11,738] [INFO] Task succeeded: CheckM
[2023-06-17 11:09:11,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:09:11,761] [INFO] ===== Completeness check finished =====
[2023-06-17 11:09:11,761] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:09:11,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003020945.1_ASM302094v1_genomic.fna/markers.fasta)
[2023-06-17 11:09:11,762] [INFO] Task started: Blastn
[2023-06-17 11:09:11,762] [INFO] Running command: blastn -query GCA_003020945.1_ASM302094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f8f432c-6473-437c-b8c3-0ca9ae9ba4e0/dqc_reference/reference_markers_gtdb.fasta -out GCA_003020945.1_ASM302094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:09:12,290] [INFO] Task succeeded: Blastn
[2023-06-17 11:09:12,295] [INFO] Selected 7 target genomes.
[2023-06-17 11:09:12,295] [INFO] Target genome list was writen to GCA_003020945.1_ASM302094v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:09:12,306] [INFO] Task started: fastANI
[2023-06-17 11:09:12,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca96a43-dd00-4433-91fc-b266114c03df/GCA_003020945.1_ASM302094v1_genomic.fna.gz --refList GCA_003020945.1_ASM302094v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003020945.1_ASM302094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:09:18,386] [INFO] Task succeeded: fastANI
[2023-06-17 11:09:18,403] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:09:18,404] [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_003020945.1	s__Halobaculum sp003020945	100.0	866	868	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009831625.1	s__Halobaculum sp009831625	84.8541	680	868	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	84.0352	665	868	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	80.9034	579	868	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	80.8793	571	868	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	80.8465	553	868	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018609965.1	s__Halobaculum sp018609965	78.0045	281	868	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:09:18,406] [INFO] GTDB search result was written to GCA_003020945.1_ASM302094v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:09:18,407] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:09:18,412] [INFO] DFAST_QC result json was written to GCA_003020945.1_ASM302094v1_genomic.fna/dqc_result.json
[2023-06-17 11:09:18,412] [INFO] DFAST_QC completed!
[2023-06-17 11:09:18,412] [INFO] Total running time: 0h1m3s