[2024-01-25 19:49:35,596] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:35,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:35,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dd4719d-dd20-4839-a19c-e48844a7b917/dqc_reference
[2024-01-25 19:49:36,701] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:36,701] [INFO] Task started: Prodigal
[2024-01-25 19:49:36,702] [INFO] Running command: gunzip -c /var/lib/cwl/stg98ed59fc-133b-4165-bc67-7770908c99e3/GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/cds.fna -a GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:51,600] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:51,601] [INFO] Task started: HMMsearch
[2024-01-25 19:49:51,601] [INFO] Running command: hmmsearch --tblout GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dd4719d-dd20-4839-a19c-e48844a7b917/dqc_reference/reference_markers.hmm GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:51,816] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:51,817] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg98ed59fc-133b-4165-bc67-7770908c99e3/GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna.gz]
[2024-01-25 19:49:51,845] [INFO] Query marker FASTA was written to GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:49:51,845] [INFO] Task started: Blastn
[2024-01-25 19:49:51,845] [INFO] Running command: blastn -query GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dd4719d-dd20-4839-a19c-e48844a7b917/dqc_reference/reference_markers.fasta -out GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:52,373] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:52,376] [INFO] Selected 13 target genomes.
[2024-01-25 19:49:52,376] [INFO] Target genome list was writen to GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:49:52,396] [INFO] Task started: fastANI
[2024-01-25 19:49:52,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg98ed59fc-133b-4165-bc67-7770908c99e3/GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna.gz --refList GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:01,881] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:01,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dd4719d-dd20-4839-a19c-e48844a7b917/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:01,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dd4719d-dd20-4839-a19c-e48844a7b917/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:01,890] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:50:01,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:50:01,891] [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 halodurans	strain=Cb34	GCA_002252985.1	1383851	1383851	type	True	80.2682	464	1123	95	below_threshold
Halorubrum cibi	strain=DSM 19504	GCA_900182635.1	413815	413815	type	True	80.2606	496	1123	95	below_threshold
Halorubrum aquaticum	strain=CGMCC 1.6377	GCA_900113615.1	387340	387340	type	True	80.2567	495	1123	95	below_threshold
Halorubrum rubrum	strain=YC87	GCA_024494685.1	1126240	1126240	type	True	80.096	509	1123	95	below_threshold
Halorubrum depositum	strain=Y78	GCA_007671725.1	2583992	2583992	type	True	80.0791	498	1123	95	below_threshold
Halorubrum saccharovorum	strain=DSM 1137	GCA_000337915.1	2248	2248	type	True	80.0034	477	1123	95	below_threshold
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	79.871	476	1123	95	below_threshold
Halorubrum salipaludis	strain=WN019	GCA_002286985.1	2032630	2032630	type	True	79.8688	498	1123	95	below_threshold
Halorubrum rutilum	strain=YJ-18-S1	GCA_024494565.1	1364933	1364933	type	True	79.8667	503	1123	95	below_threshold
Halorubrum arcis	strain=JCM 13916	GCA_000337015.1	368454	368454	type	True	79.8225	494	1123	95	below_threshold
Halorubrum aidingense	strain=JCM 13560	GCA_000336995.1	368623	368623	type	True	79.7857	496	1123	95	below_threshold
Halorubrum persicum	strain=C49	GCA_002727125.1	1383844	1383844	type	True	79.694	482	1123	95	below_threshold
Halorubrum salinum	strain=GX71	GCA_024494575.1	767517	767517	type	True	79.5471	429	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:01,895] [INFO] DFAST Taxonomy check result was written to GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:50:01,895] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:01,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:01,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dd4719d-dd20-4839-a19c-e48844a7b917/dqc_reference/checkm_data
[2024-01-25 19:50:01,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:01,932] [INFO] Task started: CheckM
[2024-01-25 19:50:01,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/checkm_input GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:50:44,032] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:44,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:44,055] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:44,055] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:44,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:50:44,056] [INFO] Task started: Blastn
[2024-01-25 19:50:44,056] [INFO] Running command: blastn -query GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dd4719d-dd20-4839-a19c-e48844a7b917/dqc_reference/reference_markers_gtdb.fasta -out GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:44,544] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:44,546] [INFO] Selected 11 target genomes.
[2024-01-25 19:50:44,547] [INFO] Target genome list was writen to GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:44,556] [INFO] Task started: fastANI
[2024-01-25 19:50:44,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg98ed59fc-133b-4165-bc67-7770908c99e3/GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna.gz --refList GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:52,651] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:52,659] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:52,659] [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_900188065.1	s__Halorubrum vacuolatum	100.0	1117	1123	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003554605.1	s__Halorubrum sp003554605	87.7194	579	1123	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.64	99.64	0.93	0.93	2	-
GCF_009806985.1	s__Halorubrum sp009806985	80.964	561	1123	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	80.2653	466	1123	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	80.1105	494	1123	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009742825.1	s__Halorubrum sp009742825	80.0731	365	1123	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	80.0364	513	1123	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286985.1	s__Halorubrum sp002286985	79.9042	495	1123	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.74	98.74	0.87	0.87	2	-
GCF_000337375.1	s__Halorubrum lipolyticum	79.857	478	1123	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000336995.1	s__Halorubrum aidingense	79.7889	495	1123	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	79.737	478	1123	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:52,661] [INFO] GTDB search result was written to GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:52,661] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:52,664] [INFO] DFAST_QC result json was written to GCF_900188065.1_IMG-taxon_2724679803_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:50:52,664] [INFO] DFAST_QC completed!
[2024-01-25 19:50:52,664] [INFO] Total running time: 0h1m17s