[2024-01-25 20:15:50,628] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:50,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:50,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg4310a0b5-a7cf-41a1-9372-7f41abcd8580/dqc_reference
[2024-01-25 20:15:51,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:51,761] [INFO] Task started: Prodigal
[2024-01-25 20:15:51,761] [INFO] Running command: gunzip -c /var/lib/cwl/stg5882a43c-ce85-4e42-a107-389bfc85cab6/GCF_003989795.1_ASM398979v1_genomic.fna.gz | prodigal -d GCF_003989795.1_ASM398979v1_genomic.fna/cds.fna -a GCF_003989795.1_ASM398979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:00,674] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:00,675] [INFO] Task started: HMMsearch
[2024-01-25 20:16:00,675] [INFO] Running command: hmmsearch --tblout GCF_003989795.1_ASM398979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4310a0b5-a7cf-41a1-9372-7f41abcd8580/dqc_reference/reference_markers.hmm GCF_003989795.1_ASM398979v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:00,911] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:00,912] [INFO] Found 6/6 markers.
[2024-01-25 20:16:00,943] [INFO] Query marker FASTA was written to GCF_003989795.1_ASM398979v1_genomic.fna/markers.fasta
[2024-01-25 20:16:00,943] [INFO] Task started: Blastn
[2024-01-25 20:16:00,943] [INFO] Running command: blastn -query GCF_003989795.1_ASM398979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4310a0b5-a7cf-41a1-9372-7f41abcd8580/dqc_reference/reference_markers.fasta -out GCF_003989795.1_ASM398979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:01,546] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:01,550] [INFO] Selected 15 target genomes.
[2024-01-25 20:16:01,550] [INFO] Target genome list was writen to GCF_003989795.1_ASM398979v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:01,555] [INFO] Task started: fastANI
[2024-01-25 20:16:01,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg5882a43c-ce85-4e42-a107-389bfc85cab6/GCF_003989795.1_ASM398979v1_genomic.fna.gz --refList GCF_003989795.1_ASM398979v1_genomic.fna/target_genomes.txt --output GCF_003989795.1_ASM398979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:11,619] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:11,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4310a0b5-a7cf-41a1-9372-7f41abcd8580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:11,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4310a0b5-a7cf-41a1-9372-7f41abcd8580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:11,628] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:16:11,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:11,628] [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
Halomonas andesensis	strain=DSM 19434	GCA_003989795.1	447567	447567	type	True	100.0	1286	1289	95	conclusive
Halomonas humidisoli	strain=WN018	GCA_002286955.1	2032624	2032624	type	True	85.9468	941	1289	95	below_threshold
Halomonas alkaliphila	strain=DSM 16354	GCA_016107625.1	272774	272774	type	True	85.9033	960	1289	95	below_threshold
Halomonas venusta	strain=NBRC 102221	GCA_007989605.1	44935	44935	type	True	85.0104	872	1289	95	below_threshold
Halomonas venusta	strain=DSM 4743	GCA_016107635.1	44935	44935	type	True	84.9701	907	1289	95	below_threshold
Halomonas hydrothermalis	strain=Slthf2	GCA_011399095.1	115561	115561	type	True	84.9389	863	1289	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.4574	353	1289	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	78.778	366	1289	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	78.7208	374	1289	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.1279	120	1289	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.0436	118	1289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:11,629] [INFO] DFAST Taxonomy check result was written to GCF_003989795.1_ASM398979v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:11,630] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:11,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:11,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4310a0b5-a7cf-41a1-9372-7f41abcd8580/dqc_reference/checkm_data
[2024-01-25 20:16:11,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:11,669] [INFO] Task started: CheckM
[2024-01-25 20:16:11,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003989795.1_ASM398979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003989795.1_ASM398979v1_genomic.fna/checkm_input GCF_003989795.1_ASM398979v1_genomic.fna/checkm_result
[2024-01-25 20:16:41,018] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:41,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:41,032] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:41,032] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:41,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003989795.1_ASM398979v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:41,033] [INFO] Task started: Blastn
[2024-01-25 20:16:41,033] [INFO] Running command: blastn -query GCF_003989795.1_ASM398979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4310a0b5-a7cf-41a1-9372-7f41abcd8580/dqc_reference/reference_markers_gtdb.fasta -out GCF_003989795.1_ASM398979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:41,906] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:41,908] [INFO] Selected 11 target genomes.
[2024-01-25 20:16:41,908] [INFO] Target genome list was writen to GCF_003989795.1_ASM398979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:41,928] [INFO] Task started: fastANI
[2024-01-25 20:16:41,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg5882a43c-ce85-4e42-a107-389bfc85cab6/GCF_003989795.1_ASM398979v1_genomic.fna.gz --refList GCF_003989795.1_ASM398979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003989795.1_ASM398979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:50,963] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:50,968] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:50,969] [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_003989795.1	s__Halomonas andesensis	100.0	1286	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000219565.1	s__Halomonas sp000219565	87.1608	960	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082565.1	s__Halomonas sp002082565	86.0018	946	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107625.1	s__Halomonas alkaliphila	85.9033	960	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	96.32	95.46	0.84	0.80	12	-
GCF_007989605.1	s__Halomonas venusta	85.0104	872	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.80	96.64	0.92	0.83	8	-
GCF_000712975.1	s__Halomonas alkaliantarctica_A	84.2254	919	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415115.1	s__Halomonas zhaodongensis	83.1172	804	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.15	99.15	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:50,971] [INFO] GTDB search result was written to GCF_003989795.1_ASM398979v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:50,971] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:50,974] [INFO] DFAST_QC result json was written to GCF_003989795.1_ASM398979v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:50,975] [INFO] DFAST_QC completed!
[2024-01-25 20:16:50,975] [INFO] Total running time: 0h1m0s