[2024-01-24 13:49:40,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,048] [INFO] DQC Reference Directory: /var/lib/cwl/stgd581528d-3ad5-4027-a1e1-f6dbb684a004/dqc_reference
[2024-01-24 13:49:41,127] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,128] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,128] [INFO] Running command: gunzip -c /var/lib/cwl/stg755af1fb-3c0b-4877-9f3b-6984c496c5fd/GCF_011762035.1_ASM1176203v1_genomic.fna.gz | prodigal -d GCF_011762035.1_ASM1176203v1_genomic.fna/cds.fna -a GCF_011762035.1_ASM1176203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:50,824] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:50,825] [INFO] Task started: HMMsearch
[2024-01-24 13:49:50,825] [INFO] Running command: hmmsearch --tblout GCF_011762035.1_ASM1176203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd581528d-3ad5-4027-a1e1-f6dbb684a004/dqc_reference/reference_markers.hmm GCF_011762035.1_ASM1176203v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:51,015] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:51,016] [INFO] Found 6/6 markers.
[2024-01-24 13:49:51,043] [INFO] Query marker FASTA was written to GCF_011762035.1_ASM1176203v1_genomic.fna/markers.fasta
[2024-01-24 13:49:51,044] [INFO] Task started: Blastn
[2024-01-24 13:49:51,044] [INFO] Running command: blastn -query GCF_011762035.1_ASM1176203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd581528d-3ad5-4027-a1e1-f6dbb684a004/dqc_reference/reference_markers.fasta -out GCF_011762035.1_ASM1176203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,993] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,995] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:51,995] [INFO] Target genome list was writen to GCF_011762035.1_ASM1176203v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:52,002] [INFO] Task started: fastANI
[2024-01-24 13:49:52,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg755af1fb-3c0b-4877-9f3b-6984c496c5fd/GCF_011762035.1_ASM1176203v1_genomic.fna.gz --refList GCF_011762035.1_ASM1176203v1_genomic.fna/target_genomes.txt --output GCF_011762035.1_ASM1176203v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:04,506] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd581528d-3ad5-4027-a1e1-f6dbb684a004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:04,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd581528d-3ad5-4027-a1e1-f6dbb684a004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:04,516] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:04,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:04,516] [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
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	100.0	1234	1236	95	conclusive
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	99.9936	1228	1236	95	conclusive
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	85.0307	833	1236	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	83.9914	805	1236	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	83.9748	738	1236	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	83.889	820	1236	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	81.232	690	1236	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	80.9734	680	1236	95	below_threshold
Sphingomonas aurantiaca	strain=MA101b	GCA_003050705.1	185949	185949	type	True	80.5735	682	1236	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.2379	613	1236	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	79.966	552	1236	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.9639	564	1236	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.9504	615	1236	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.6965	552	1236	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.679	548	1236	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,518] [INFO] DFAST Taxonomy check result was written to GCF_011762035.1_ASM1176203v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:04,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:04,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:04,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd581528d-3ad5-4027-a1e1-f6dbb684a004/dqc_reference/checkm_data
[2024-01-24 13:50:04,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:04,556] [INFO] Task started: CheckM
[2024-01-24 13:50:04,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011762035.1_ASM1176203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011762035.1_ASM1176203v1_genomic.fna/checkm_input GCF_011762035.1_ASM1176203v1_genomic.fna/checkm_result
[2024-01-24 13:50:35,398] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:35,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:35,415] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:35,415] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:35,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011762035.1_ASM1176203v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:35,416] [INFO] Task started: Blastn
[2024-01-24 13:50:35,416] [INFO] Running command: blastn -query GCF_011762035.1_ASM1176203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd581528d-3ad5-4027-a1e1-f6dbb684a004/dqc_reference/reference_markers_gtdb.fasta -out GCF_011762035.1_ASM1176203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:37,363] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:37,366] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:37,366] [INFO] Target genome list was writen to GCF_011762035.1_ASM1176203v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:37,376] [INFO] Task started: fastANI
[2024-01-24 13:50:37,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg755af1fb-3c0b-4877-9f3b-6984c496c5fd/GCF_011762035.1_ASM1176203v1_genomic.fna.gz --refList GCF_011762035.1_ASM1176203v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011762035.1_ASM1176203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:48,371] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:48,380] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:48,380] [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_010450875.1	s__Sphingomonas insulae	99.9936	1228	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_002292295.1	s__Sphingomonas sp002292295	87.3826	902	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	85.0072	814	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	85.0035	835	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_000632225.1	s__Sphingomonas sp000632225	84.1825	794	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196115.1	s__Sphingomonas aquatilis	83.9912	805	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCA_003075315.1	s__Sphingomonas sp003075315	83.7862	803	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCF_001421505.1	s__Sphingomonas sp001421505	80.4857	626	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422045.1	s__Sphingomonas sp001422045	80.2959	628	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014358075.1	s__Sphingomonas albertensis	80.1607	603	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304635.1	s__Sphingomonas sp017304635	79.9622	525	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110035.1	s__Sphingomonas gellani	79.9461	554	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745215.1	s__Sphingomonas sp017745215	78.9443	498	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:48,381] [INFO] GTDB search result was written to GCF_011762035.1_ASM1176203v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:48,381] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:48,384] [INFO] DFAST_QC result json was written to GCF_011762035.1_ASM1176203v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:48,384] [INFO] DFAST_QC completed!
[2024-01-24 13:50:48,384] [INFO] Total running time: 0h1m8s