[2024-01-25 18:07:50,499] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:50,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:50,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf754684-0005-43cf-8220-d07d99db1299/dqc_reference
[2024-01-25 18:07:51,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:51,622] [INFO] Task started: Prodigal
[2024-01-25 18:07:51,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg512273a5-eda0-4b9b-b946-cfecb7e4364e/GCF_013415905.1_ASM1341590v1_genomic.fna.gz | prodigal -d GCF_013415905.1_ASM1341590v1_genomic.fna/cds.fna -a GCF_013415905.1_ASM1341590v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:11,508] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:11,508] [INFO] Task started: HMMsearch
[2024-01-25 18:08:11,508] [INFO] Running command: hmmsearch --tblout GCF_013415905.1_ASM1341590v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf754684-0005-43cf-8220-d07d99db1299/dqc_reference/reference_markers.hmm GCF_013415905.1_ASM1341590v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:11,746] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:11,747] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg512273a5-eda0-4b9b-b946-cfecb7e4364e/GCF_013415905.1_ASM1341590v1_genomic.fna.gz]
[2024-01-25 18:08:11,788] [INFO] Query marker FASTA was written to GCF_013415905.1_ASM1341590v1_genomic.fna/markers.fasta
[2024-01-25 18:08:11,789] [INFO] Task started: Blastn
[2024-01-25 18:08:11,789] [INFO] Running command: blastn -query GCF_013415905.1_ASM1341590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf754684-0005-43cf-8220-d07d99db1299/dqc_reference/reference_markers.fasta -out GCF_013415905.1_ASM1341590v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:12,290] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:12,294] [INFO] Selected 5 target genomes.
[2024-01-25 18:08:12,294] [INFO] Target genome list was writen to GCF_013415905.1_ASM1341590v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:12,299] [INFO] Task started: fastANI
[2024-01-25 18:08:12,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg512273a5-eda0-4b9b-b946-cfecb7e4364e/GCF_013415905.1_ASM1341590v1_genomic.fna.gz --refList GCF_013415905.1_ASM1341590v1_genomic.fna/target_genomes.txt --output GCF_013415905.1_ASM1341590v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:21,230] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:21,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf754684-0005-43cf-8220-d07d99db1299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:21,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf754684-0005-43cf-8220-d07d99db1299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:21,236] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:21,236] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:21,236] [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
Halosimplex pelagicum	strain=R2	GCA_013415905.1	869886	869886	type	True	100.0	1724	1733	95	conclusive
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	91.8918	1183	1733	95	below_threshold
Halosimplex carlsbadense	strain=2-9-1	GCA_000337455.1	171164	171164	type	True	90.168	1125	1733	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	89.7103	1137	1733	95	below_threshold
Halosimplex litoreum	strain=YGH94	GCA_016065055.1	1198301	1198301	type	True	89.4379	1091	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:21,237] [INFO] DFAST Taxonomy check result was written to GCF_013415905.1_ASM1341590v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:21,238] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:21,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:21,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf754684-0005-43cf-8220-d07d99db1299/dqc_reference/checkm_data
[2024-01-25 18:08:21,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:21,290] [INFO] Task started: CheckM
[2024-01-25 18:08:21,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013415905.1_ASM1341590v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013415905.1_ASM1341590v1_genomic.fna/checkm_input GCF_013415905.1_ASM1341590v1_genomic.fna/checkm_result
[2024-01-25 18:09:13,569] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:13,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:13,587] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:13,587] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:13,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013415905.1_ASM1341590v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:13,587] [INFO] Task started: Blastn
[2024-01-25 18:09:13,588] [INFO] Running command: blastn -query GCF_013415905.1_ASM1341590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf754684-0005-43cf-8220-d07d99db1299/dqc_reference/reference_markers_gtdb.fasta -out GCF_013415905.1_ASM1341590v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:14,164] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:14,167] [INFO] Selected 5 target genomes.
[2024-01-25 18:09:14,167] [INFO] Target genome list was writen to GCF_013415905.1_ASM1341590v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:14,176] [INFO] Task started: fastANI
[2024-01-25 18:09:14,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg512273a5-eda0-4b9b-b946-cfecb7e4364e/GCF_013415905.1_ASM1341590v1_genomic.fna.gz --refList GCF_013415905.1_ASM1341590v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013415905.1_ASM1341590v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:23,158] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:23,163] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:23,163] [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_013415905.1	s__Halosimplex pelagicum	100.0	1728	1733	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013415885.1	s__Halosimplex rubrum	91.8167	1189	1733	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337455.1	s__Halosimplex carlsbadense	90.1352	1127	1733	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004698125.1	s__Halosimplex halophilum	89.675	1139	1733	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016065055.1	s__Halosimplex litoreum	89.4515	1090	1733	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:23,164] [INFO] GTDB search result was written to GCF_013415905.1_ASM1341590v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:23,165] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:23,167] [INFO] DFAST_QC result json was written to GCF_013415905.1_ASM1341590v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:23,167] [INFO] DFAST_QC completed!
[2024-01-25 18:09:23,167] [INFO] Total running time: 0h1m33s