[2024-01-25 18:10:21,084] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:21,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:21,086] [INFO] DQC Reference Directory: /var/lib/cwl/stgab95f541-9eb9-4dcb-a82a-62b03c065d84/dqc_reference
[2024-01-25 18:10:22,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:22,261] [INFO] Task started: Prodigal
[2024-01-25 18:10:22,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg84994d45-aefd-417b-82c3-cc1654a917cb/GCF_003342675.1_ASM334267v1_genomic.fna.gz | prodigal -d GCF_003342675.1_ASM334267v1_genomic.fna/cds.fna -a GCF_003342675.1_ASM334267v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:38,240] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:38,240] [INFO] Task started: HMMsearch
[2024-01-25 18:10:38,240] [INFO] Running command: hmmsearch --tblout GCF_003342675.1_ASM334267v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab95f541-9eb9-4dcb-a82a-62b03c065d84/dqc_reference/reference_markers.hmm GCF_003342675.1_ASM334267v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:38,442] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:38,443] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg84994d45-aefd-417b-82c3-cc1654a917cb/GCF_003342675.1_ASM334267v1_genomic.fna.gz]
[2024-01-25 18:10:38,478] [INFO] Query marker FASTA was written to GCF_003342675.1_ASM334267v1_genomic.fna/markers.fasta
[2024-01-25 18:10:38,479] [INFO] Task started: Blastn
[2024-01-25 18:10:38,479] [INFO] Running command: blastn -query GCF_003342675.1_ASM334267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab95f541-9eb9-4dcb-a82a-62b03c065d84/dqc_reference/reference_markers.fasta -out GCF_003342675.1_ASM334267v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:39,004] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:39,006] [INFO] Selected 5 target genomes.
[2024-01-25 18:10:39,007] [INFO] Target genome list was writen to GCF_003342675.1_ASM334267v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:39,010] [INFO] Task started: fastANI
[2024-01-25 18:10:39,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg84994d45-aefd-417b-82c3-cc1654a917cb/GCF_003342675.1_ASM334267v1_genomic.fna.gz --refList GCF_003342675.1_ASM334267v1_genomic.fna/target_genomes.txt --output GCF_003342675.1_ASM334267v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:44,339] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:44,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab95f541-9eb9-4dcb-a82a-62b03c065d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:44,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab95f541-9eb9-4dcb-a82a-62b03c065d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:44,344] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:44,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:44,345] [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
Haloplanus rubicundus	strain=CBA1112	GCA_003342675.1	1547898	1547898	type	True	100.0	1257	1257	95	conclusive
Haloplanus salinus	strain=JCM 18368	GCA_003336245.1	1126245	1126245	type	True	90.2653	880	1257	95	below_threshold
Haloplanus natans	strain=DSM 17983	GCA_000427685.1	376171	376171	type	True	87.7258	856	1257	95	below_threshold
Haloplanus aerogenes	strain=CGMCC 1.10124	GCA_003688715.1	660522	660522	type	True	86.842	855	1257	95	below_threshold
Haloplanus aerogenes	strain=JCM 16430	GCA_003856835.1	660522	660522	type	True	86.8055	859	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:44,346] [INFO] DFAST Taxonomy check result was written to GCF_003342675.1_ASM334267v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:44,346] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:44,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:44,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab95f541-9eb9-4dcb-a82a-62b03c065d84/dqc_reference/checkm_data
[2024-01-25 18:10:44,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:44,389] [INFO] Task started: CheckM
[2024-01-25 18:10:44,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003342675.1_ASM334267v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003342675.1_ASM334267v1_genomic.fna/checkm_input GCF_003342675.1_ASM334267v1_genomic.fna/checkm_result
[2024-01-25 18:11:27,256] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:27,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:27,274] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:27,274] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:27,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003342675.1_ASM334267v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:27,275] [INFO] Task started: Blastn
[2024-01-25 18:11:27,275] [INFO] Running command: blastn -query GCF_003342675.1_ASM334267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab95f541-9eb9-4dcb-a82a-62b03c065d84/dqc_reference/reference_markers_gtdb.fasta -out GCF_003342675.1_ASM334267v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:27,847] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:27,850] [INFO] Selected 6 target genomes.
[2024-01-25 18:11:27,850] [INFO] Target genome list was writen to GCF_003342675.1_ASM334267v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:27,856] [INFO] Task started: fastANI
[2024-01-25 18:11:27,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg84994d45-aefd-417b-82c3-cc1654a917cb/GCF_003342675.1_ASM334267v1_genomic.fna.gz --refList GCF_003342675.1_ASM334267v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003342675.1_ASM334267v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:34,110] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:34,116] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:34,116] [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_003342675.1	s__Haloplanus rubicundus	100.0	1257	1257	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	98.71	98.71	0.88	0.88	2	conclusive
GCF_003336245.1	s__Haloplanus salinus	90.2637	880	1257	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427685.1	s__Haloplanus natans	87.7725	853	1257	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856835.1	s__Haloplanus aerogenes	86.7797	861	1257	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009762275.1	s__Haloplanus rallus	84.7803	766	1257	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107665.1	s__Haloplanus vescus	84.2755	667	1257	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:34,118] [INFO] GTDB search result was written to GCF_003342675.1_ASM334267v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:34,119] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:34,122] [INFO] DFAST_QC result json was written to GCF_003342675.1_ASM334267v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:34,123] [INFO] DFAST_QC completed!
[2024-01-25 18:11:34,123] [INFO] Total running time: 0h1m13s