[2024-01-25 18:08:35,585] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:35,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:35,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg6cc063e1-b6bb-47da-b799-553a67f6c5b4/dqc_reference
[2024-01-25 18:08:36,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:36,798] [INFO] Task started: Prodigal
[2024-01-25 18:08:36,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg76f218c8-dcae-4d9f-9fce-1bccd385a489/GCF_026262645.1_ASM2626264v1_genomic.fna.gz | prodigal -d GCF_026262645.1_ASM2626264v1_genomic.fna/cds.fna -a GCF_026262645.1_ASM2626264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:47,240] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:47,240] [INFO] Task started: HMMsearch
[2024-01-25 18:08:47,240] [INFO] Running command: hmmsearch --tblout GCF_026262645.1_ASM2626264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6cc063e1-b6bb-47da-b799-553a67f6c5b4/dqc_reference/reference_markers.hmm GCF_026262645.1_ASM2626264v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:47,457] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:47,458] [INFO] Found 6/6 markers.
[2024-01-25 18:08:47,489] [INFO] Query marker FASTA was written to GCF_026262645.1_ASM2626264v1_genomic.fna/markers.fasta
[2024-01-25 18:08:47,489] [INFO] Task started: Blastn
[2024-01-25 18:08:47,489] [INFO] Running command: blastn -query GCF_026262645.1_ASM2626264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cc063e1-b6bb-47da-b799-553a67f6c5b4/dqc_reference/reference_markers.fasta -out GCF_026262645.1_ASM2626264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:48,119] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:48,122] [INFO] Selected 33 target genomes.
[2024-01-25 18:08:48,123] [INFO] Target genome list was writen to GCF_026262645.1_ASM2626264v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:48,152] [INFO] Task started: fastANI
[2024-01-25 18:08:48,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg76f218c8-dcae-4d9f-9fce-1bccd385a489/GCF_026262645.1_ASM2626264v1_genomic.fna.gz --refList GCF_026262645.1_ASM2626264v1_genomic.fna/target_genomes.txt --output GCF_026262645.1_ASM2626264v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:12,270] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:12,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6cc063e1-b6bb-47da-b799-553a67f6c5b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:12,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6cc063e1-b6bb-47da-b799-553a67f6c5b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:12,279] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:09:12,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:09:12,279] [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
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.2603	110	1355	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.9098	110	1355	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.7319	80	1355	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.5867	95	1355	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.5751	110	1355	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.5741	93	1355	95	below_threshold
Sediminihaliea albiluteola	strain=F7430	GCA_014077625.1	2758564	2758564	type	True	76.5164	61	1355	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.4929	81	1355	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.3749	81	1355	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.3729	83	1355	95	below_threshold
Halioglobus pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	76.1036	78	1355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:12,280] [INFO] DFAST Taxonomy check result was written to GCF_026262645.1_ASM2626264v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:12,281] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:12,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:12,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6cc063e1-b6bb-47da-b799-553a67f6c5b4/dqc_reference/checkm_data
[2024-01-25 18:09:12,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:12,322] [INFO] Task started: CheckM
[2024-01-25 18:09:12,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026262645.1_ASM2626264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026262645.1_ASM2626264v1_genomic.fna/checkm_input GCF_026262645.1_ASM2626264v1_genomic.fna/checkm_result
[2024-01-25 18:09:45,423] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:45,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:45,443] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:45,443] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:45,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026262645.1_ASM2626264v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:45,444] [INFO] Task started: Blastn
[2024-01-25 18:09:45,444] [INFO] Running command: blastn -query GCF_026262645.1_ASM2626264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cc063e1-b6bb-47da-b799-553a67f6c5b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_026262645.1_ASM2626264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:46,526] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:46,528] [INFO] Selected 29 target genomes.
[2024-01-25 18:09:46,528] [INFO] Target genome list was writen to GCF_026262645.1_ASM2626264v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:46,558] [INFO] Task started: fastANI
[2024-01-25 18:09:46,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg76f218c8-dcae-4d9f-9fce-1bccd385a489/GCF_026262645.1_ASM2626264v1_genomic.fna.gz --refList GCF_026262645.1_ASM2626264v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026262645.1_ASM2626264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:07,196] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:07,205] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:10:07,206] [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_905480565.1	s__Halioglobus sp905480565	89.9109	710	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	77.1588	143	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_004354085.1	s__Halioglobus sp004354085	76.9115	109	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	76.8396	82	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	76.7319	80	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704305.1	s__Halioglobus sp016704305	76.632	137	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCF_008064665.1	s__Parahaliea maris	76.5921	96	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705825.1	s__Halioglobus japonicus_A	76.5292	123	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077625.1	s__Parahaliea sp014077625	76.4762	61	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214285.1	s__Halioglobus sp013214285	76.4728	115	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	76.462	81	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCA_009937575.1	s__Halioglobus sp009937575	76.3562	122	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646415.1	s__Halioglobus sp003646415	76.3053	68	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:07,207] [INFO] GTDB search result was written to GCF_026262645.1_ASM2626264v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:07,208] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:07,210] [INFO] DFAST_QC result json was written to GCF_026262645.1_ASM2626264v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:07,210] [INFO] DFAST_QC completed!
[2024-01-25 18:10:07,211] [INFO] Total running time: 0h1m32s