[2024-01-24 14:54:56,662] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d2b3dc3-66f0-4376-95e8-1eb24ed6bfe2/dqc_reference
[2024-01-24 14:54:58,123] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:58,124] [INFO] Task started: Prodigal
[2024-01-24 14:54:58,124] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5011340-86ba-4388-820c-8a5d48a155cf/GCF_012427705.1_ASM1242770v1_genomic.fna.gz | prodigal -d GCF_012427705.1_ASM1242770v1_genomic.fna/cds.fna -a GCF_012427705.1_ASM1242770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:10,645] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:10,646] [INFO] Task started: HMMsearch
[2024-01-24 14:55:10,646] [INFO] Running command: hmmsearch --tblout GCF_012427705.1_ASM1242770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d2b3dc3-66f0-4376-95e8-1eb24ed6bfe2/dqc_reference/reference_markers.hmm GCF_012427705.1_ASM1242770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:10,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:10,980] [INFO] Found 6/6 markers.
[2024-01-24 14:55:11,021] [INFO] Query marker FASTA was written to GCF_012427705.1_ASM1242770v1_genomic.fna/markers.fasta
[2024-01-24 14:55:11,021] [INFO] Task started: Blastn
[2024-01-24 14:55:11,021] [INFO] Running command: blastn -query GCF_012427705.1_ASM1242770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d2b3dc3-66f0-4376-95e8-1eb24ed6bfe2/dqc_reference/reference_markers.fasta -out GCF_012427705.1_ASM1242770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:11,852] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:11,855] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:11,855] [INFO] Target genome list was writen to GCF_012427705.1_ASM1242770v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:11,859] [INFO] Task started: fastANI
[2024-01-24 14:55:11,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5011340-86ba-4388-820c-8a5d48a155cf/GCF_012427705.1_ASM1242770v1_genomic.fna.gz --refList GCF_012427705.1_ASM1242770v1_genomic.fna/target_genomes.txt --output GCF_012427705.1_ASM1242770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:20,757] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:20,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d2b3dc3-66f0-4376-95e8-1eb24ed6bfe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:20,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d2b3dc3-66f0-4376-95e8-1eb24ed6bfe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:20,768] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:55:20,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:20,769] [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 piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	100.0	1314	1315	95	conclusive
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	99.9688	1275	1315	95	conclusive
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	87.6446	845	1315	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	87.6195	885	1315	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	87.5533	838	1315	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	84.5285	951	1315	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	79.5576	459	1315	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.4217	441	1315	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.6603	347	1315	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.2829	305	1315	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.7918	287	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:20,770] [INFO] DFAST Taxonomy check result was written to GCF_012427705.1_ASM1242770v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:20,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:20,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:20,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d2b3dc3-66f0-4376-95e8-1eb24ed6bfe2/dqc_reference/checkm_data
[2024-01-24 14:55:20,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:20,816] [INFO] Task started: CheckM
[2024-01-24 14:55:20,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012427705.1_ASM1242770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012427705.1_ASM1242770v1_genomic.fna/checkm_input GCF_012427705.1_ASM1242770v1_genomic.fna/checkm_result
[2024-01-24 14:55:59,712] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:59,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:59,737] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:59,737] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:59,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012427705.1_ASM1242770v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:59,738] [INFO] Task started: Blastn
[2024-01-24 14:55:59,738] [INFO] Running command: blastn -query GCF_012427705.1_ASM1242770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d2b3dc3-66f0-4376-95e8-1eb24ed6bfe2/dqc_reference/reference_markers_gtdb.fasta -out GCF_012427705.1_ASM1242770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:01,151] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:01,155] [INFO] Selected 8 target genomes.
[2024-01-24 14:56:01,155] [INFO] Target genome list was writen to GCF_012427705.1_ASM1242770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:01,163] [INFO] Task started: fastANI
[2024-01-24 14:56:01,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5011340-86ba-4388-820c-8a5d48a155cf/GCF_012427705.1_ASM1242770v1_genomic.fna.gz --refList GCF_012427705.1_ASM1242770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012427705.1_ASM1242770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:08,291] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:08,304] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:08,304] [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_012427705.1	s__Halomonas piezotolerans	100.0	1313	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	conclusive
GCF_009846525.1	s__Halomonas sp002696125	88.1649	1039	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_900110265.1	s__Halomonas aquamarina	87.6443	845	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_002087295.1	s__Halomonas lionensis	85.5614	844	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640815.1	s__Halomonas lutescens	84.5346	950	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651775.1	s__Halomonas hamiltonii	82.9743	836	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_000275725.1	s__Halomonas stevensii	82.9052	787	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_003002925.1	s__Halomonas songnenensis	80.0008	593	1315	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 14:56:08,306] [INFO] GTDB search result was written to GCF_012427705.1_ASM1242770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:08,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:08,310] [INFO] DFAST_QC result json was written to GCF_012427705.1_ASM1242770v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:08,310] [INFO] DFAST_QC completed!
[2024-01-24 14:56:08,310] [INFO] Total running time: 0h1m12s