[2024-01-24 11:12:48,737] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:48,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:48,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgef4e41fb-3fc8-4517-a9b5-09979e28bbe2/dqc_reference
[2024-01-24 11:12:49,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:49,918] [INFO] Task started: Prodigal
[2024-01-24 11:12:49,919] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3fa5815-1a5b-4865-9650-ca5e6d8bbea8/GCF_007421925.1_ASM742192v1_genomic.fna.gz | prodigal -d GCF_007421925.1_ASM742192v1_genomic.fna/cds.fna -a GCF_007421925.1_ASM742192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:09,517] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:09,517] [INFO] Task started: HMMsearch
[2024-01-24 11:13:09,517] [INFO] Running command: hmmsearch --tblout GCF_007421925.1_ASM742192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef4e41fb-3fc8-4517-a9b5-09979e28bbe2/dqc_reference/reference_markers.hmm GCF_007421925.1_ASM742192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:09,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:09,764] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd3fa5815-1a5b-4865-9650-ca5e6d8bbea8/GCF_007421925.1_ASM742192v1_genomic.fna.gz]
[2024-01-24 11:13:09,799] [INFO] Query marker FASTA was written to GCF_007421925.1_ASM742192v1_genomic.fna/markers.fasta
[2024-01-24 11:13:09,800] [INFO] Task started: Blastn
[2024-01-24 11:13:09,800] [INFO] Running command: blastn -query GCF_007421925.1_ASM742192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef4e41fb-3fc8-4517-a9b5-09979e28bbe2/dqc_reference/reference_markers.fasta -out GCF_007421925.1_ASM742192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:10,321] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:10,324] [INFO] Selected 9 target genomes.
[2024-01-24 11:13:10,325] [INFO] Target genome list was writen to GCF_007421925.1_ASM742192v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:10,334] [INFO] Task started: fastANI
[2024-01-24 11:13:10,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3fa5815-1a5b-4865-9650-ca5e6d8bbea8/GCF_007421925.1_ASM742192v1_genomic.fna.gz --refList GCF_007421925.1_ASM742192v1_genomic.fna/target_genomes.txt --output GCF_007421925.1_ASM742192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:18,286] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:18,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef4e41fb-3fc8-4517-a9b5-09979e28bbe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:18,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef4e41fb-3fc8-4517-a9b5-09979e28bbe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:18,297] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:18,297] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:18,297] [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
Haloglomus irregulare	strain=F16-60	GCA_007421925.1	2234134	2234134	type	True	100.0	1308	1311	95	conclusive
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	78.853	540	1311	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	78.8477	480	1311	95	below_threshold
Halomarina salina	strain=ZS-57-S	GCA_023074835.1	1872699	1872699	type	True	78.2655	423	1311	95	below_threshold
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	78.155	375	1311	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	78.0539	448	1311	95	below_threshold
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	77.8388	351	1311	95	below_threshold
Halosimplex pelagicum	strain=R2	GCA_013415905.1	869886	869886	type	True	77.7196	465	1311	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	77.6729	492	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:18,299] [INFO] DFAST Taxonomy check result was written to GCF_007421925.1_ASM742192v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:18,300] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:18,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:18,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef4e41fb-3fc8-4517-a9b5-09979e28bbe2/dqc_reference/checkm_data
[2024-01-24 11:13:18,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:18,341] [INFO] Task started: CheckM
[2024-01-24 11:13:18,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007421925.1_ASM742192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007421925.1_ASM742192v1_genomic.fna/checkm_input GCF_007421925.1_ASM742192v1_genomic.fna/checkm_result
[2024-01-24 11:14:10,992] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:10,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:11,015] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:11,015] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:11,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007421925.1_ASM742192v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:11,016] [INFO] Task started: Blastn
[2024-01-24 11:14:11,016] [INFO] Running command: blastn -query GCF_007421925.1_ASM742192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef4e41fb-3fc8-4517-a9b5-09979e28bbe2/dqc_reference/reference_markers_gtdb.fasta -out GCF_007421925.1_ASM742192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:11,525] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:11,530] [INFO] Selected 9 target genomes.
[2024-01-24 11:14:11,530] [INFO] Target genome list was writen to GCF_007421925.1_ASM742192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:11,543] [INFO] Task started: fastANI
[2024-01-24 11:14:11,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3fa5815-1a5b-4865-9650-ca5e6d8bbea8/GCF_007421925.1_ASM742192v1_genomic.fna.gz --refList GCF_007421925.1_ASM742192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007421925.1_ASM742192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:18,511] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:18,524] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:18,524] [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_007421925.1	s__Haloglomus irregulare	100.0	1308	1311	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloglomus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003020985.1	s__Haloglomus sp003020985	83.4942	694	1311	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloglomus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	78.839	481	1311	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018609665.1	s__Natronomonas sp018609665	78.4253	396	1311	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022005.1	s__QS-5-70-15 sp003022005	78.2839	403	1311	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-5-70-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020965.1	s__Natronomonas sp003020965	78.2337	436	1311	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415885.1	s__Halosimplex rubrum	78.0278	451	1311	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415905.1	s__Halosimplex pelagicum	77.7269	464	1311	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007135435.1	s__Natronomonas sp007135435	77.7213	276	1311	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:18,526] [INFO] GTDB search result was written to GCF_007421925.1_ASM742192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:18,526] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:18,529] [INFO] DFAST_QC result json was written to GCF_007421925.1_ASM742192v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:18,529] [INFO] DFAST_QC completed!
[2024-01-24 11:14:18,529] [INFO] Total running time: 0h1m30s