[2024-01-25 18:55:35,751] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:35,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:35,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg954b5f24-4c3e-4eeb-9f7d-2e476692a0a1/dqc_reference
[2024-01-25 18:55:36,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:36,880] [INFO] Task started: Prodigal
[2024-01-25 18:55:36,881] [INFO] Running command: gunzip -c /var/lib/cwl/stg3973e2bf-e6c7-47c6-acc4-417826aaf050/GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna.gz | prodigal -d GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/cds.fna -a GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:46,640] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:46,640] [INFO] Task started: HMMsearch
[2024-01-25 18:55:46,640] [INFO] Running command: hmmsearch --tblout GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg954b5f24-4c3e-4eeb-9f7d-2e476692a0a1/dqc_reference/reference_markers.hmm GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:46,888] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:46,889] [INFO] Found 6/6 markers.
[2024-01-25 18:55:46,941] [INFO] Query marker FASTA was written to GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/markers.fasta
[2024-01-25 18:55:46,942] [INFO] Task started: Blastn
[2024-01-25 18:55:46,942] [INFO] Running command: blastn -query GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/markers.fasta -db /var/lib/cwl/stg954b5f24-4c3e-4eeb-9f7d-2e476692a0a1/dqc_reference/reference_markers.fasta -out GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:47,802] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:47,805] [INFO] Selected 15 target genomes.
[2024-01-25 18:55:47,805] [INFO] Target genome list was writen to GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/target_genomes.txt
[2024-01-25 18:55:47,829] [INFO] Task started: fastANI
[2024-01-25 18:55:47,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg3973e2bf-e6c7-47c6-acc4-417826aaf050/GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna.gz --refList GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/target_genomes.txt --output GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:00,788] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:00,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg954b5f24-4c3e-4eeb-9f7d-2e476692a0a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:00,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg954b5f24-4c3e-4eeb-9f7d-2e476692a0a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:00,799] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:00,799] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:00,799] [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
Sphingobium bisphenolivorans	strain=YL23	GCA_000412635.1	1335760	1335760	type	True	100.0	1235	1236	95	conclusive
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	84.4913	759	1236	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	84.3348	752	1236	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	84.1553	781	1236	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	84.0584	790	1236	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	83.9479	656	1236	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	83.868	708	1236	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	83.8106	706	1236	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	82.9914	660	1236	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	82.0991	700	1236	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	78.21	300	1236	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.0569	328	1236	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.0042	305	1236	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.6116	338	1236	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.5421	273	1236	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:00,800] [INFO] DFAST Taxonomy check result was written to GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/tc_result.tsv
[2024-01-25 18:56:00,801] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:00,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:00,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg954b5f24-4c3e-4eeb-9f7d-2e476692a0a1/dqc_reference/checkm_data
[2024-01-25 18:56:00,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:00,840] [INFO] Task started: CheckM
[2024-01-25 18:56:00,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/checkm_input GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/checkm_result
[2024-01-25 18:56:31,639] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:31,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:31,659] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:31,659] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:31,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/markers.fasta)
[2024-01-25 18:56:31,660] [INFO] Task started: Blastn
[2024-01-25 18:56:31,660] [INFO] Running command: blastn -query GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/markers.fasta -db /var/lib/cwl/stg954b5f24-4c3e-4eeb-9f7d-2e476692a0a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:33,325] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:33,340] [INFO] Selected 13 target genomes.
[2024-01-25 18:56:33,340] [INFO] Target genome list was writen to GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:33,348] [INFO] Task started: fastANI
[2024-01-25 18:56:33,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg3973e2bf-e6c7-47c6-acc4-417826aaf050/GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna.gz --refList GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/target_genomes_gtdb.txt --output GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:46,427] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:46,435] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:46,436] [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_000412635.1	s__Sphingobium bisphenolivorans	100.0	1235	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001005725.1	s__Sphingobium chungbukense	84.4583	763	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCA_000264945.2	s__Sphingobium indicum	84.3554	751	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_001563265.1	s__Sphingobium sp001563265	84.2184	796	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.38	97.84	0.74	0.68	3	-
GCF_004152845.1	s__Sphingobium fuliginis	84.1731	779	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_013375555.1	s__Sphingobium sp013375555	84.023	738	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375535.1	s__Sphingobium sp013375535	83.9728	776	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	83.8688	709	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_008692605.1	s__Sphingobium estronivorans	83.8074	706	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873695.1	s__Sphingobium sp014873695	83.5077	774	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445065.1	s__Sphingobium quisquiliarum	83.0067	658	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	-
GCF_001658005.1	s__Sphingobium sp001658005	82.1768	710	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197035.1	s__Sphingobium scionense	82.1281	698	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:46,437] [INFO] GTDB search result was written to GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:46,437] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:46,440] [INFO] DFAST_QC result json was written to GCF_000412635.1_Sphingobium_sp._strain_YL23_genomic.fna/dqc_result.json
[2024-01-25 18:56:46,440] [INFO] DFAST_QC completed!
[2024-01-25 18:56:46,440] [INFO] Total running time: 0h1m11s