[2024-01-24 13:32:42,169] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,173] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6216706-d37e-4f8c-8d3a-4f820a09a872/dqc_reference
[2024-01-24 13:32:43,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,514] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c013156-5b01-4513-864a-1ae4e0eef305/GCF_017094525.1_ASM1709452v1_genomic.fna.gz | prodigal -d GCF_017094525.1_ASM1709452v1_genomic.fna/cds.fna -a GCF_017094525.1_ASM1709452v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:57,621] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:57,621] [INFO] Task started: HMMsearch
[2024-01-24 13:32:57,621] [INFO] Running command: hmmsearch --tblout GCF_017094525.1_ASM1709452v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6216706-d37e-4f8c-8d3a-4f820a09a872/dqc_reference/reference_markers.hmm GCF_017094525.1_ASM1709452v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:57,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:57,888] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5c013156-5b01-4513-864a-1ae4e0eef305/GCF_017094525.1_ASM1709452v1_genomic.fna.gz]
[2024-01-24 13:32:57,917] [INFO] Query marker FASTA was written to GCF_017094525.1_ASM1709452v1_genomic.fna/markers.fasta
[2024-01-24 13:32:57,917] [INFO] Task started: Blastn
[2024-01-24 13:32:57,918] [INFO] Running command: blastn -query GCF_017094525.1_ASM1709452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6216706-d37e-4f8c-8d3a-4f820a09a872/dqc_reference/reference_markers.fasta -out GCF_017094525.1_ASM1709452v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:58,474] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:58,477] [INFO] Selected 7 target genomes.
[2024-01-24 13:32:58,478] [INFO] Target genome list was writen to GCF_017094525.1_ASM1709452v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:58,481] [INFO] Task started: fastANI
[2024-01-24 13:32:58,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c013156-5b01-4513-864a-1ae4e0eef305/GCF_017094525.1_ASM1709452v1_genomic.fna.gz --refList GCF_017094525.1_ASM1709452v1_genomic.fna/target_genomes.txt --output GCF_017094525.1_ASM1709452v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:04,728] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:04,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6216706-d37e-4f8c-8d3a-4f820a09a872/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:04,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6216706-d37e-4f8c-8d3a-4f820a09a872/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:04,736] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:04,737] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:04,737] [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
Halapricum desulfuricans	strain=HSR12-2	GCA_017094525.1	2841257	2841257	type	True	100.0	964	964	95	conclusive
Halapricum salinum	strain=CBA1105	GCA_004799665.1	1457250	1457250	type	True	80.6073	495	964	95	below_threshold
Halapricum salinum	strain=CBA1105	GCA_000755225.1	1457250	1457250	type	True	80.4731	509	964	95	below_threshold
Halorhabdus tiamatea	strain=SARL4B	GCA_000215915.3	430914	430914	type	True	79.0799	333	964	95	below_threshold
Halorhabdus tiamatea	strain=type strain: SARL4B	GCA_000470655.1	430914	430914	type	True	78.9489	358	964	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	78.2559	376	964	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	77.881	328	964	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:04,745] [INFO] DFAST Taxonomy check result was written to GCF_017094525.1_ASM1709452v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:04,745] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:04,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:04,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6216706-d37e-4f8c-8d3a-4f820a09a872/dqc_reference/checkm_data
[2024-01-24 13:33:04,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:04,777] [INFO] Task started: CheckM
[2024-01-24 13:33:04,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017094525.1_ASM1709452v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017094525.1_ASM1709452v1_genomic.fna/checkm_input GCF_017094525.1_ASM1709452v1_genomic.fna/checkm_result
[2024-01-24 13:33:46,972] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:46,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:46,992] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:46,993] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:46,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017094525.1_ASM1709452v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:46,993] [INFO] Task started: Blastn
[2024-01-24 13:33:46,993] [INFO] Running command: blastn -query GCF_017094525.1_ASM1709452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6216706-d37e-4f8c-8d3a-4f820a09a872/dqc_reference/reference_markers_gtdb.fasta -out GCF_017094525.1_ASM1709452v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:47,485] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:47,488] [INFO] Selected 6 target genomes.
[2024-01-24 13:33:47,488] [INFO] Target genome list was writen to GCF_017094525.1_ASM1709452v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:47,495] [INFO] Task started: fastANI
[2024-01-24 13:33:47,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c013156-5b01-4513-864a-1ae4e0eef305/GCF_017094525.1_ASM1709452v1_genomic.fna.gz --refList GCF_017094525.1_ASM1709452v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017094525.1_ASM1709452v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:52,346] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:52,353] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:52,353] [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_017094525.1	s__Halapricum sp017094525	100.0	964	964	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum	95.0	98.12	98.12	0.88	0.88	2	conclusive
GCA_017094505.1	s__Halapricum sp017094505	93.5743	764	964	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017094465.1	s__Halapricum sp017094465	85.1819	676	964	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799665.1	s__Halapricum salinum	80.617	495	964	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009741825.1	s__Halapricum sp009741825	79.3099	393	964	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004698125.1	s__Halosimplex halophilum	78.2353	378	964	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:52,354] [INFO] GTDB search result was written to GCF_017094525.1_ASM1709452v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:52,355] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:52,358] [INFO] DFAST_QC result json was written to GCF_017094525.1_ASM1709452v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:52,358] [INFO] DFAST_QC completed!
[2024-01-24 13:33:52,358] [INFO] Total running time: 0h1m10s