[2024-01-24 15:26:47,759] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:47,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:47,761] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa719e6c-8025-47d5-98a0-ab7a87c902bb/dqc_reference
[2024-01-24 15:26:48,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:48,957] [INFO] Task started: Prodigal
[2024-01-24 15:26:48,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f6bc3df-7f82-4137-b13a-714112ebe381/GCF_003201605.1_ASM320160v1_genomic.fna.gz | prodigal -d GCF_003201605.1_ASM320160v1_genomic.fna/cds.fna -a GCF_003201605.1_ASM320160v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:54,153] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:54,154] [INFO] Task started: HMMsearch
[2024-01-24 15:26:54,154] [INFO] Running command: hmmsearch --tblout GCF_003201605.1_ASM320160v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa719e6c-8025-47d5-98a0-ab7a87c902bb/dqc_reference/reference_markers.hmm GCF_003201605.1_ASM320160v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:54,388] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:54,389] [INFO] Found 6/6 markers.
[2024-01-24 15:26:54,422] [INFO] Query marker FASTA was written to GCF_003201605.1_ASM320160v1_genomic.fna/markers.fasta
[2024-01-24 15:26:54,422] [INFO] Task started: Blastn
[2024-01-24 15:26:54,423] [INFO] Running command: blastn -query GCF_003201605.1_ASM320160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa719e6c-8025-47d5-98a0-ab7a87c902bb/dqc_reference/reference_markers.fasta -out GCF_003201605.1_ASM320160v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:55,001] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:55,008] [INFO] Selected 21 target genomes.
[2024-01-24 15:26:55,009] [INFO] Target genome list was writen to GCF_003201605.1_ASM320160v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:55,454] [INFO] Task started: fastANI
[2024-01-24 15:26:55,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f6bc3df-7f82-4137-b13a-714112ebe381/GCF_003201605.1_ASM320160v1_genomic.fna.gz --refList GCF_003201605.1_ASM320160v1_genomic.fna/target_genomes.txt --output GCF_003201605.1_ASM320160v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:07,524] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:07,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa719e6c-8025-47d5-98a0-ab7a87c902bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:07,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa719e6c-8025-47d5-98a0-ab7a87c902bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:07,541] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:07,541] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:07,541] [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
Streptohalobacillus salinus	strain=DSM 22440	GCA_003201605.1	621096	621096	type	True	100.0	824	825	95	conclusive
Halolactibacillus miurensis	strain=DSM 17074	GCA_900116255.1	306541	306541	type	True	78.91	215	825	95	below_threshold
Halolactibacillus miurensis	strain=NBRC 100873	GCA_007990305.1	306541	306541	type	True	78.8122	212	825	95	below_threshold
Halolactibacillus halophilus	strain=DSM 17073	GCA_900115605.1	306540	306540	type	True	78.6082	189	825	95	below_threshold
Halolactibacillus halophilus	strain=NBRC 100868	GCA_007990285.1	306540	306540	type	True	78.4964	186	825	95	below_threshold
Amphibacillus marinus	strain=CGMCC 1.10434	GCA_900110345.1	872970	872970	type	True	78.2465	103	825	95	below_threshold
Pelagirhabdus alkalitolerans	strain=S5	GCA_900096905.1	1612202	1612202	type	True	78.2317	117	825	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.941	77	825	95	below_threshold
Amphibacillus cookii	strain=DSM 23721	GCA_016908375.1	767787	767787	type	True	77.8947	106	825	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	77.3721	55	825	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:07,543] [INFO] DFAST Taxonomy check result was written to GCF_003201605.1_ASM320160v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:07,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:07,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:07,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa719e6c-8025-47d5-98a0-ab7a87c902bb/dqc_reference/checkm_data
[2024-01-24 15:27:07,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:07,570] [INFO] Task started: CheckM
[2024-01-24 15:27:07,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201605.1_ASM320160v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201605.1_ASM320160v1_genomic.fna/checkm_input GCF_003201605.1_ASM320160v1_genomic.fna/checkm_result
[2024-01-24 15:27:30,862] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:30,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:30,877] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:30,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:30,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201605.1_ASM320160v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:30,879] [INFO] Task started: Blastn
[2024-01-24 15:27:30,879] [INFO] Running command: blastn -query GCF_003201605.1_ASM320160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa719e6c-8025-47d5-98a0-ab7a87c902bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201605.1_ASM320160v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:31,630] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:31,634] [INFO] Selected 22 target genomes.
[2024-01-24 15:27:31,634] [INFO] Target genome list was writen to GCF_003201605.1_ASM320160v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:31,649] [INFO] Task started: fastANI
[2024-01-24 15:27:31,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f6bc3df-7f82-4137-b13a-714112ebe381/GCF_003201605.1_ASM320160v1_genomic.fna.gz --refList GCF_003201605.1_ASM320160v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201605.1_ASM320160v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:45,800] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:45,808] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:45,808] [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_003201605.1	s__Streptohalobacillus salinus	100.0	824	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Streptohalobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900116255.1	s__Halolactibacillus miurensis	78.91	215	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.76	99.51	0.98	0.95	3	-
GCF_900115605.1	s__Halolactibacillus halophilus	78.5997	190	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900096905.1	s__Pelagirhabdus alkalitolerans	78.2649	116	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pelagirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110345.1	s__Amphibacillus_D marinus	78.2465	103	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	77.941	77	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306965.1	s__Amphibacillus_C jilinensis	77.9272	110	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908375.1	s__Amphibacillus_C cookii	77.8947	106	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:45,810] [INFO] GTDB search result was written to GCF_003201605.1_ASM320160v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:45,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:45,814] [INFO] DFAST_QC result json was written to GCF_003201605.1_ASM320160v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:45,814] [INFO] DFAST_QC completed!
[2024-01-24 15:27:45,814] [INFO] Total running time: 0h0m58s