[2024-01-24 13:37:10,281] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:10,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:10,285] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3fe8335-43a6-43d0-b06c-5156df17fc40/dqc_reference
[2024-01-24 13:37:11,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:11,568] [INFO] Task started: Prodigal
[2024-01-24 13:37:11,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg921cf774-0e55-4e6b-ab43-eaa3d07690d7/GCF_011399095.1_ASM1139909v1_genomic.fna.gz | prodigal -d GCF_011399095.1_ASM1139909v1_genomic.fna/cds.fna -a GCF_011399095.1_ASM1139909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:24,800] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:24,800] [INFO] Task started: HMMsearch
[2024-01-24 13:37:24,800] [INFO] Running command: hmmsearch --tblout GCF_011399095.1_ASM1139909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3fe8335-43a6-43d0-b06c-5156df17fc40/dqc_reference/reference_markers.hmm GCF_011399095.1_ASM1139909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:25,105] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:25,107] [INFO] Found 6/6 markers.
[2024-01-24 13:37:25,142] [INFO] Query marker FASTA was written to GCF_011399095.1_ASM1139909v1_genomic.fna/markers.fasta
[2024-01-24 13:37:25,143] [INFO] Task started: Blastn
[2024-01-24 13:37:25,143] [INFO] Running command: blastn -query GCF_011399095.1_ASM1139909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3fe8335-43a6-43d0-b06c-5156df17fc40/dqc_reference/reference_markers.fasta -out GCF_011399095.1_ASM1139909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:25,855] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:25,858] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:25,859] [INFO] Target genome list was writen to GCF_011399095.1_ASM1139909v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:25,883] [INFO] Task started: fastANI
[2024-01-24 13:37:25,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg921cf774-0e55-4e6b-ab43-eaa3d07690d7/GCF_011399095.1_ASM1139909v1_genomic.fna.gz --refList GCF_011399095.1_ASM1139909v1_genomic.fna/target_genomes.txt --output GCF_011399095.1_ASM1139909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:35,723] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3fe8335-43a6-43d0-b06c-5156df17fc40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:35,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3fe8335-43a6-43d0-b06c-5156df17fc40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:35,734] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:37:35,735] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:37:35,735] [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 hydrothermalis	strain=Slthf2	GCA_011399095.1	115561	115561	type	True	100.0	1369	1373	95	inconclusive
Halomonas venusta	strain=DSM 4743	GCA_016107635.1	44935	44935	type	True	96.6238	1153	1373	95	inconclusive
Halomonas venusta	strain=NBRC 102221	GCA_007989605.1	44935	44935	type	True	96.6059	1141	1373	95	inconclusive
Halomonas alkaliphila	strain=DSM 16354	GCA_016107625.1	272774	272774	type	True	92.8784	1096	1373	95	below_threshold
Halomonas humidisoli	strain=WN018	GCA_002286955.1	2032624	2032624	type	True	92.7884	1076	1373	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.0827	415	1373	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.8511	128	1373	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.834	138	1373	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.5077	127	1373	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	76.9831	154	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,737] [INFO] DFAST Taxonomy check result was written to GCF_011399095.1_ASM1139909v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:35,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:35,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:35,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3fe8335-43a6-43d0-b06c-5156df17fc40/dqc_reference/checkm_data
[2024-01-24 13:37:35,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:35,785] [INFO] Task started: CheckM
[2024-01-24 13:37:35,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011399095.1_ASM1139909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011399095.1_ASM1139909v1_genomic.fna/checkm_input GCF_011399095.1_ASM1139909v1_genomic.fna/checkm_result
[2024-01-24 13:38:18,551] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:18,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:18,569] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:18,569] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:18,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011399095.1_ASM1139909v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:18,569] [INFO] Task started: Blastn
[2024-01-24 13:38:18,570] [INFO] Running command: blastn -query GCF_011399095.1_ASM1139909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3fe8335-43a6-43d0-b06c-5156df17fc40/dqc_reference/reference_markers_gtdb.fasta -out GCF_011399095.1_ASM1139909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:19,633] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:19,637] [INFO] Selected 6 target genomes.
[2024-01-24 13:38:19,637] [INFO] Target genome list was writen to GCF_011399095.1_ASM1139909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:19,679] [INFO] Task started: fastANI
[2024-01-24 13:38:19,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg921cf774-0e55-4e6b-ab43-eaa3d07690d7/GCF_011399095.1_ASM1139909v1_genomic.fna.gz --refList GCF_011399095.1_ASM1139909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011399095.1_ASM1139909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:25,419] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:25,425] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:25,425] [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_007989605.1	s__Halomonas venusta	96.6059	1141	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.80	96.64	0.92	0.83	8	conclusive
GCF_016107625.1	s__Halomonas alkaliphila	92.8784	1096	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	96.32	95.46	0.84	0.80	12	-
GCF_002082565.1	s__Halomonas sp002082565	90.117	1077	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219565.1	s__Halomonas sp000219565	88.5393	1042	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712975.1	s__Halomonas alkaliantarctica_A	85.8229	916	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003989795.1	s__Halomonas andesensis	84.9039	881	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:25,427] [INFO] GTDB search result was written to GCF_011399095.1_ASM1139909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:25,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:25,430] [INFO] DFAST_QC result json was written to GCF_011399095.1_ASM1139909v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:25,430] [INFO] DFAST_QC completed!
[2024-01-24 13:38:25,430] [INFO] Total running time: 0h1m15s