[2024-01-25 17:40:05,499] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:05,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:05,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8942954-0b15-4523-8d24-7c40ff3097ab/dqc_reference
[2024-01-25 17:40:06,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:06,689] [INFO] Task started: Prodigal
[2024-01-25 17:40:06,690] [INFO] Running command: gunzip -c /var/lib/cwl/stga7dc513c-f28d-4dbd-9c05-8eccf870ace2/GCF_026262685.1_ASM2626268v1_genomic.fna.gz | prodigal -d GCF_026262685.1_ASM2626268v1_genomic.fna/cds.fna -a GCF_026262685.1_ASM2626268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:18,051] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:18,052] [INFO] Task started: HMMsearch
[2024-01-25 17:40:18,052] [INFO] Running command: hmmsearch --tblout GCF_026262685.1_ASM2626268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8942954-0b15-4523-8d24-7c40ff3097ab/dqc_reference/reference_markers.hmm GCF_026262685.1_ASM2626268v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:18,333] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:18,334] [INFO] Found 6/6 markers.
[2024-01-25 17:40:18,373] [INFO] Query marker FASTA was written to GCF_026262685.1_ASM2626268v1_genomic.fna/markers.fasta
[2024-01-25 17:40:18,373] [INFO] Task started: Blastn
[2024-01-25 17:40:18,373] [INFO] Running command: blastn -query GCF_026262685.1_ASM2626268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8942954-0b15-4523-8d24-7c40ff3097ab/dqc_reference/reference_markers.fasta -out GCF_026262685.1_ASM2626268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:19,025] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:19,032] [INFO] Selected 18 target genomes.
[2024-01-25 17:40:19,032] [INFO] Target genome list was writen to GCF_026262685.1_ASM2626268v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:19,040] [INFO] Task started: fastANI
[2024-01-25 17:40:19,041] [INFO] Running command: fastANI --query /var/lib/cwl/stga7dc513c-f28d-4dbd-9c05-8eccf870ace2/GCF_026262685.1_ASM2626268v1_genomic.fna.gz --refList GCF_026262685.1_ASM2626268v1_genomic.fna/target_genomes.txt --output GCF_026262685.1_ASM2626268v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:31,845] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:31,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8942954-0b15-4523-8d24-7c40ff3097ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:31,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8942954-0b15-4523-8d24-7c40ff3097ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:31,855] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:40:31,855] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:40:31,855] [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
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.8105	300	1441	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.719	281	1441	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	77.5846	178	1441	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.5338	185	1441	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.404	186	1441	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	77.38	186	1441	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.1126	121	1441	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.9217	126	1441	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.7545	121	1441	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.731	90	1441	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.5692	86	1441	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	76.5628	56	1441	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.519	56	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:31,857] [INFO] DFAST Taxonomy check result was written to GCF_026262685.1_ASM2626268v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:31,857] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:31,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:31,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8942954-0b15-4523-8d24-7c40ff3097ab/dqc_reference/checkm_data
[2024-01-25 17:40:31,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:31,899] [INFO] Task started: CheckM
[2024-01-25 17:40:31,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026262685.1_ASM2626268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026262685.1_ASM2626268v1_genomic.fna/checkm_input GCF_026262685.1_ASM2626268v1_genomic.fna/checkm_result
[2024-01-25 17:41:08,285] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:08,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:08,334] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:08,334] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:08,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026262685.1_ASM2626268v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:08,335] [INFO] Task started: Blastn
[2024-01-25 17:41:08,335] [INFO] Running command: blastn -query GCF_026262685.1_ASM2626268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8942954-0b15-4523-8d24-7c40ff3097ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_026262685.1_ASM2626268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:09,493] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:09,496] [INFO] Selected 17 target genomes.
[2024-01-25 17:41:09,496] [INFO] Target genome list was writen to GCF_026262685.1_ASM2626268v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:09,511] [INFO] Task started: fastANI
[2024-01-25 17:41:09,512] [INFO] Running command: fastANI --query /var/lib/cwl/stga7dc513c-f28d-4dbd-9c05-8eccf870ace2/GCF_026262685.1_ASM2626268v1_genomic.fna.gz --refList GCF_026262685.1_ASM2626268v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026262685.1_ASM2626268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:22,187] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:22,195] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:22,196] [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_000156295.1	s__Halioglobus sp000156295	97.652	1283	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.94	98.78	0.94	0.91	6	conclusive
GCA_004354085.1	s__Halioglobus sp004354085	77.8015	300	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	77.7094	281	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009388985.1	s__Halioglobus maricola	77.5846	178	1441	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	77.5259	184	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_008370495.1	s__Halioglobus sp008370495	77.5007	192	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	77.1126	121	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862985.1	s__Halioglobus sp002862985	76.6313	57	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002868715.1	s__Kineobactrum sediminis	76.5911	85	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	76.584	101	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_004340525.1	s__Chromatocurvus halotolerans	76.519	56	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002692965.1	s__NZNC01 sp002692965	76.3208	74	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCA_002416125.1	s__Haliea sp002416125	76.0806	83	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:22,198] [INFO] GTDB search result was written to GCF_026262685.1_ASM2626268v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:22,198] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:22,201] [INFO] DFAST_QC result json was written to GCF_026262685.1_ASM2626268v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:22,201] [INFO] DFAST_QC completed!
[2024-01-25 17:41:22,201] [INFO] Total running time: 0h1m17s