[2024-01-25 18:40:35,601] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:35,613] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:35,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgd282c409-12b7-4086-8929-8cd0950adba6/dqc_reference
[2024-01-25 18:40:36,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:36,761] [INFO] Task started: Prodigal
[2024-01-25 18:40:36,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg619797e5-0044-4e41-8932-267be838c70a/GCF_023638035.1_ASM2363803v1_genomic.fna.gz | prodigal -d GCF_023638035.1_ASM2363803v1_genomic.fna/cds.fna -a GCF_023638035.1_ASM2363803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:53,566] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:53,567] [INFO] Task started: HMMsearch
[2024-01-25 18:40:53,567] [INFO] Running command: hmmsearch --tblout GCF_023638035.1_ASM2363803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd282c409-12b7-4086-8929-8cd0950adba6/dqc_reference/reference_markers.hmm GCF_023638035.1_ASM2363803v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:53,756] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:53,757] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg619797e5-0044-4e41-8932-267be838c70a/GCF_023638035.1_ASM2363803v1_genomic.fna.gz]
[2024-01-25 18:40:53,787] [INFO] Query marker FASTA was written to GCF_023638035.1_ASM2363803v1_genomic.fna/markers.fasta
[2024-01-25 18:40:53,787] [INFO] Task started: Blastn
[2024-01-25 18:40:53,787] [INFO] Running command: blastn -query GCF_023638035.1_ASM2363803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd282c409-12b7-4086-8929-8cd0950adba6/dqc_reference/reference_markers.fasta -out GCF_023638035.1_ASM2363803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:54,237] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:54,240] [INFO] Selected 10 target genomes.
[2024-01-25 18:40:54,240] [INFO] Target genome list was writen to GCF_023638035.1_ASM2363803v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:54,243] [INFO] Task started: fastANI
[2024-01-25 18:40:54,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg619797e5-0044-4e41-8932-267be838c70a/GCF_023638035.1_ASM2363803v1_genomic.fna.gz --refList GCF_023638035.1_ASM2363803v1_genomic.fna/target_genomes.txt --output GCF_023638035.1_ASM2363803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:00,357] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:00,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd282c409-12b7-4086-8929-8cd0950adba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:00,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd282c409-12b7-4086-8929-8cd0950adba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:00,363] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:00,363] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:00,363] [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
Natronocalculus amylovorans	strain=AArc-St2	GCA_023638035.1	2917812	2917812	type	True	100.0	1073	1075	95	conclusive
Halalkalirubrum salinum	strain=N1521	GCA_005543295.1	2563889	2563889	type	True	76.9347	154	1075	95	below_threshold
Halohasta litchfieldiae	strain=tADL	GCA_002788215.1	1073996	1073996	type	True	76.8243	77	1075	95	below_threshold
Halonotius pteroides	strain=CECT 7525	GCA_003605635.1	268735	268735	type	True	76.5406	56	1075	95	below_threshold
Halonotius roseus	strain=F9-27	GCA_006861655.1	2511997	2511997	type	True	76.0707	57	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:00,366] [INFO] DFAST Taxonomy check result was written to GCF_023638035.1_ASM2363803v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:00,366] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:00,367] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:00,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd282c409-12b7-4086-8929-8cd0950adba6/dqc_reference/checkm_data
[2024-01-25 18:41:00,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:00,401] [INFO] Task started: CheckM
[2024-01-25 18:41:00,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023638035.1_ASM2363803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023638035.1_ASM2363803v1_genomic.fna/checkm_input GCF_023638035.1_ASM2363803v1_genomic.fna/checkm_result
[2024-01-25 18:41:50,668] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:50,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:50,697] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:50,697] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:50,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023638035.1_ASM2363803v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:50,698] [INFO] Task started: Blastn
[2024-01-25 18:41:50,698] [INFO] Running command: blastn -query GCF_023638035.1_ASM2363803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd282c409-12b7-4086-8929-8cd0950adba6/dqc_reference/reference_markers_gtdb.fasta -out GCF_023638035.1_ASM2363803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:51,176] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:51,179] [INFO] Selected 10 target genomes.
[2024-01-25 18:41:51,179] [INFO] Target genome list was writen to GCF_023638035.1_ASM2363803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:51,185] [INFO] Task started: fastANI
[2024-01-25 18:41:51,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg619797e5-0044-4e41-8932-267be838c70a/GCF_023638035.1_ASM2363803v1_genomic.fna.gz --refList GCF_023638035.1_ASM2363803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023638035.1_ASM2363803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:57,216] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:57,220] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:57,221] [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
GCA_013342525.1	s__Halalkalirubrum sp003551725	98.3738	956	1075	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halalkalirubrum	95.0	98.81	98.81	0.76	0.76	2	conclusive
GCA_005239175.1	s__Halalkalirubrum sp005239175	77.0056	152	1075	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halalkalirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005543295.1	s__Halalkalirubrum salinum	76.9347	154	1075	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halalkalirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605635.1	s__Halonotius pteroides	76.5406	56	1075	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861655.1	s__Halonotius roseus	76.0707	57	1075	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:57,223] [INFO] GTDB search result was written to GCF_023638035.1_ASM2363803v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:57,223] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:57,227] [INFO] DFAST_QC result json was written to GCF_023638035.1_ASM2363803v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:57,227] [INFO] DFAST_QC completed!
[2024-01-25 18:41:57,227] [INFO] Total running time: 0h1m22s