[2024-01-24 13:17:15,360] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgd275cf74-cdf7-4afd-8eb8-2c4f5d5c664a/dqc_reference
[2024-01-24 13:17:16,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:16,783] [INFO] Task started: Prodigal
[2024-01-24 13:17:16,783] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b1755b6-c2ba-4d3b-8356-86bb782ecca4/GCF_007671685.1_ASM767168v1_genomic.fna.gz | prodigal -d GCF_007671685.1_ASM767168v1_genomic.fna/cds.fna -a GCF_007671685.1_ASM767168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:34,727] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:34,727] [INFO] Task started: HMMsearch
[2024-01-24 13:17:34,727] [INFO] Running command: hmmsearch --tblout GCF_007671685.1_ASM767168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd275cf74-cdf7-4afd-8eb8-2c4f5d5c664a/dqc_reference/reference_markers.hmm GCF_007671685.1_ASM767168v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:34,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:34,981] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0b1755b6-c2ba-4d3b-8356-86bb782ecca4/GCF_007671685.1_ASM767168v1_genomic.fna.gz]
[2024-01-24 13:17:35,024] [INFO] Query marker FASTA was written to GCF_007671685.1_ASM767168v1_genomic.fna/markers.fasta
[2024-01-24 13:17:35,024] [INFO] Task started: Blastn
[2024-01-24 13:17:35,025] [INFO] Running command: blastn -query GCF_007671685.1_ASM767168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd275cf74-cdf7-4afd-8eb8-2c4f5d5c664a/dqc_reference/reference_markers.fasta -out GCF_007671685.1_ASM767168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:35,572] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:35,574] [INFO] Selected 9 target genomes.
[2024-01-24 13:17:35,575] [INFO] Target genome list was writen to GCF_007671685.1_ASM767168v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:35,579] [INFO] Task started: fastANI
[2024-01-24 13:17:35,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b1755b6-c2ba-4d3b-8356-86bb782ecca4/GCF_007671685.1_ASM767168v1_genomic.fna.gz --refList GCF_007671685.1_ASM767168v1_genomic.fna/target_genomes.txt --output GCF_007671685.1_ASM767168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:45,895] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:45,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd275cf74-cdf7-4afd-8eb8-2c4f5d5c664a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:45,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd275cf74-cdf7-4afd-8eb8-2c4f5d5c664a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:45,904] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:45,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:45,905] [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 salsamenti	strain=Y69	GCA_007671685.1	2583990	2583990	type	True	100.0	1213	1213	95	conclusive
Halorubrum saccharovorum	strain=DSM 1137	GCA_000337915.1	2248	2248	type	True	91.1173	818	1213	95	below_threshold
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	90.888	803	1213	95	below_threshold
Halorubrum amylolyticum	strain=ZC67	GCA_004114995.1	2508724	2508724	type	True	90.8608	813	1213	95	below_threshold
Halorubrum salipaludis	strain=WN019	GCA_002286985.1	2032630	2032630	type	True	90.5506	831	1213	95	below_threshold
Halorubrum halophilum	strain=B8	GCA_000739595.1	413816	413816	type	True	90.5444	816	1213	95	below_threshold
Halorubrum kocurii	strain=JCM 14978	GCA_000337355.1	478441	478441	type	True	90.0973	788	1213	95	below_threshold
Halorubrum lacusprofundi	strain=ATCC 49239	GCA_000022205.1	2247	2247	type	True	89.6479	800	1213	95	below_threshold
Halorubrum rutilum	strain=YJ-18-S1	GCA_024494565.1	1364933	1364933	type	True	87.3326	729	1213	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:45,906] [INFO] DFAST Taxonomy check result was written to GCF_007671685.1_ASM767168v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:45,906] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:45,907] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:45,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd275cf74-cdf7-4afd-8eb8-2c4f5d5c664a/dqc_reference/checkm_data
[2024-01-24 13:17:45,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:45,951] [INFO] Task started: CheckM
[2024-01-24 13:17:45,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007671685.1_ASM767168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007671685.1_ASM767168v1_genomic.fna/checkm_input GCF_007671685.1_ASM767168v1_genomic.fna/checkm_result
[2024-01-24 13:18:34,171] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:34,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:34,195] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:34,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:34,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007671685.1_ASM767168v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:34,196] [INFO] Task started: Blastn
[2024-01-24 13:18:34,196] [INFO] Running command: blastn -query GCF_007671685.1_ASM767168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd275cf74-cdf7-4afd-8eb8-2c4f5d5c664a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007671685.1_ASM767168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:34,691] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:34,695] [INFO] Selected 9 target genomes.
[2024-01-24 13:18:34,695] [INFO] Target genome list was writen to GCF_007671685.1_ASM767168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:34,722] [INFO] Task started: fastANI
[2024-01-24 13:18:34,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b1755b6-c2ba-4d3b-8356-86bb782ecca4/GCF_007671685.1_ASM767168v1_genomic.fna.gz --refList GCF_007671685.1_ASM767168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007671685.1_ASM767168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:44,205] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:44,222] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:44,222] [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_007671685.1	s__Halorubrum salsamenti	100.0	1213	1213	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_000337915.1	s__Halorubrum saccharovorum	91.1176	818	1213	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	90.9979	806	1213	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	90.9082	802	1213	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004114995.1	s__Halorubrum amylolyticum	90.8851	812	1213	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	90.5507	831	1213	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	90.5433	816	1213	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.11	98.11	0.88	0.88	2	-
GCF_000337355.1	s__Halorubrum kocurii	90.105	787	1213	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	87.6008	812	1213	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:44,224] [INFO] GTDB search result was written to GCF_007671685.1_ASM767168v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:44,225] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:44,229] [INFO] DFAST_QC result json was written to GCF_007671685.1_ASM767168v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:44,229] [INFO] DFAST_QC completed!
[2024-01-24 13:18:44,230] [INFO] Total running time: 0h1m29s