[2024-01-24 13:36:32,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,112] [INFO] DQC Reference Directory: /var/lib/cwl/stge968ccab-c1ab-4193-84ca-2653ab2c02e4/dqc_reference
[2024-01-24 13:36:33,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,432] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,432] [INFO] Running command: gunzip -c /var/lib/cwl/stgd31bf5f1-19b8-44a9-b1db-a8a4866268a8/GCF_000336995.1_ASM33699v1_genomic.fna.gz | prodigal -d GCF_000336995.1_ASM33699v1_genomic.fna/cds.fna -a GCF_000336995.1_ASM33699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:47,787] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:47,788] [INFO] Task started: HMMsearch
[2024-01-24 13:36:47,788] [INFO] Running command: hmmsearch --tblout GCF_000336995.1_ASM33699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge968ccab-c1ab-4193-84ca-2653ab2c02e4/dqc_reference/reference_markers.hmm GCF_000336995.1_ASM33699v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:48,033] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:48,035] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd31bf5f1-19b8-44a9-b1db-a8a4866268a8/GCF_000336995.1_ASM33699v1_genomic.fna.gz]
[2024-01-24 13:36:48,066] [INFO] Query marker FASTA was written to GCF_000336995.1_ASM33699v1_genomic.fna/markers.fasta
[2024-01-24 13:36:48,067] [INFO] Task started: Blastn
[2024-01-24 13:36:48,067] [INFO] Running command: blastn -query GCF_000336995.1_ASM33699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge968ccab-c1ab-4193-84ca-2653ab2c02e4/dqc_reference/reference_markers.fasta -out GCF_000336995.1_ASM33699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:48,599] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:48,603] [INFO] Selected 11 target genomes.
[2024-01-24 13:36:48,603] [INFO] Target genome list was writen to GCF_000336995.1_ASM33699v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:48,613] [INFO] Task started: fastANI
[2024-01-24 13:36:48,614] [INFO] Running command: fastANI --query /var/lib/cwl/stgd31bf5f1-19b8-44a9-b1db-a8a4866268a8/GCF_000336995.1_ASM33699v1_genomic.fna.gz --refList GCF_000336995.1_ASM33699v1_genomic.fna/target_genomes.txt --output GCF_000336995.1_ASM33699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:58,780] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:58,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge968ccab-c1ab-4193-84ca-2653ab2c02e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:58,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge968ccab-c1ab-4193-84ca-2653ab2c02e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:58,793] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:58,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:58,794] [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 aidingense	strain=JCM 13560	GCA_000336995.1	368623	368623	type	True	100.0	1021	1022	95	conclusive
Halorubrum depositum	strain=Y78	GCA_007671725.1	2583992	2583992	type	True	86.2883	721	1022	95	below_threshold
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	86.2465	750	1022	95	below_threshold
Halorubrum salsamenti	strain=Y69	GCA_007671685.1	2583990	2583990	type	True	86.0081	719	1022	95	below_threshold
Halorubrum kocurii	strain=JCM 14978	GCA_000337355.1	478441	478441	type	True	85.9581	720	1022	95	below_threshold
Halorubrum salipaludis	strain=WN019	GCA_002286985.1	2032630	2032630	type	True	85.7678	740	1022	95	below_threshold
Halorubrum rutilum	strain=YJ-18-S1	GCA_024494565.1	1364933	1364933	type	True	85.7485	701	1022	95	below_threshold
Halorubrum persicum	strain=C49	GCA_002727125.1	1383844	1383844	type	True	85.7087	678	1022	95	below_threshold
Halorubrum halophilum	strain=B8	GCA_000739595.1	413816	413816	type	True	85.7036	715	1022	95	below_threshold
Halorubrum saccharovorum	strain=DSM 1137	GCA_000337915.1	2248	2248	type	True	85.6938	697	1022	95	below_threshold
Halorubrum amylolyticum	strain=ZC67	GCA_004114995.1	2508724	2508724	type	True	85.68	694	1022	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:58,796] [INFO] DFAST Taxonomy check result was written to GCF_000336995.1_ASM33699v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:58,797] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:58,797] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:58,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge968ccab-c1ab-4193-84ca-2653ab2c02e4/dqc_reference/checkm_data
[2024-01-24 13:36:58,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:58,831] [INFO] Task started: CheckM
[2024-01-24 13:36:58,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000336995.1_ASM33699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000336995.1_ASM33699v1_genomic.fna/checkm_input GCF_000336995.1_ASM33699v1_genomic.fna/checkm_result
[2024-01-24 13:37:43,126] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:43,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:43,144] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:43,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:43,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000336995.1_ASM33699v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:43,145] [INFO] Task started: Blastn
[2024-01-24 13:37:43,145] [INFO] Running command: blastn -query GCF_000336995.1_ASM33699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge968ccab-c1ab-4193-84ca-2653ab2c02e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000336995.1_ASM33699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:43,664] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:43,668] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:43,668] [INFO] Target genome list was writen to GCF_000336995.1_ASM33699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:43,680] [INFO] Task started: fastANI
[2024-01-24 13:37:43,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgd31bf5f1-19b8-44a9-b1db-a8a4866268a8/GCF_000336995.1_ASM33699v1_genomic.fna.gz --refList GCF_000336995.1_ASM33699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000336995.1_ASM33699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:54,739] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:54,753] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:54,754] [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_000336995.1	s__Halorubrum aidingense	100.0	1021	1022	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_007671725.1	s__Halorubrum depositum	86.2498	723	1022	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337375.1	s__Halorubrum lipolyticum	86.2268	752	1022	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007671685.1	s__Halorubrum salsamenti	86.0444	716	1022	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337355.1	s__Halorubrum kocurii	85.9865	718	1022	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721435.2	s__Halorubrum sp003721435	85.9631	738	1022	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003781945.1	s__Halorubrum sp003781945	85.8431	726	1022	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	85.7564	740	1022	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.74	98.74	0.87	0.87	2	-
GCF_000739595.1	s__Halorubrum halophilum	85.712	714	1022	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.11	98.11	0.88	0.88	2	-
GCF_000337915.1	s__Halorubrum saccharovorum	85.6931	697	1022	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	85.6862	680	1022	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252755.1	s__Halorubrum sp002252755	85.4804	720	1022	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.78	98.49	0.85	0.82	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:54,755] [INFO] GTDB search result was written to GCF_000336995.1_ASM33699v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:54,755] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:54,759] [INFO] DFAST_QC result json was written to GCF_000336995.1_ASM33699v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:54,759] [INFO] DFAST_QC completed!
[2024-01-24 13:37:54,759] [INFO] Total running time: 0h1m23s