[2024-01-25 18:13:05,632] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:05,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:05,633] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3f586f4-0c92-4f0a-b1ba-01ce3cada5c9/dqc_reference
[2024-01-25 18:13:06,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:06,775] [INFO] Task started: Prodigal
[2024-01-25 18:13:06,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg66ba44a4-7de9-45a7-b035-30bbfcdc8a93/GCF_013378075.1_ASM1337807v1_genomic.fna.gz | prodigal -d GCF_013378075.1_ASM1337807v1_genomic.fna/cds.fna -a GCF_013378075.1_ASM1337807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:16,014] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:16,015] [INFO] Task started: HMMsearch
[2024-01-25 18:13:16,015] [INFO] Running command: hmmsearch --tblout GCF_013378075.1_ASM1337807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3f586f4-0c92-4f0a-b1ba-01ce3cada5c9/dqc_reference/reference_markers.hmm GCF_013378075.1_ASM1337807v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:16,215] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:16,216] [INFO] Found 6/6 markers.
[2024-01-25 18:13:16,244] [INFO] Query marker FASTA was written to GCF_013378075.1_ASM1337807v1_genomic.fna/markers.fasta
[2024-01-25 18:13:16,244] [INFO] Task started: Blastn
[2024-01-25 18:13:16,244] [INFO] Running command: blastn -query GCF_013378075.1_ASM1337807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f586f4-0c92-4f0a-b1ba-01ce3cada5c9/dqc_reference/reference_markers.fasta -out GCF_013378075.1_ASM1337807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:17,113] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:17,115] [INFO] Selected 20 target genomes.
[2024-01-25 18:13:17,116] [INFO] Target genome list was writen to GCF_013378075.1_ASM1337807v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:17,124] [INFO] Task started: fastANI
[2024-01-25 18:13:17,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg66ba44a4-7de9-45a7-b035-30bbfcdc8a93/GCF_013378075.1_ASM1337807v1_genomic.fna.gz --refList GCF_013378075.1_ASM1337807v1_genomic.fna/target_genomes.txt --output GCF_013378075.1_ASM1337807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:32,021] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:32,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3f586f4-0c92-4f0a-b1ba-01ce3cada5c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:32,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3f586f4-0c92-4f0a-b1ba-01ce3cada5c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:32,033] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:32,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:32,034] [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
Parasphingopyxis algicola	strain=JCM 31719	GCA_013378075.1	2026624	2026624	type	True	100.0	1223	1223	95	conclusive
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	80.9458	635	1223	95	below_threshold
Parasphingopyxis lamellibrachiae	strain=DSM 26725	GCA_003385775.1	680125	680125	type	True	80.8158	673	1223	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	78.015	357	1223	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	77.9303	310	1223	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.8977	347	1223	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.797	359	1223	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	77.7629	329	1223	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	77.6871	330	1223	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.6661	324	1223	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.6132	313	1223	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	77.58	278	1223	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	77.5697	207	1223	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.4575	314	1223	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.3931	340	1223	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	77.3403	277	1223	95	below_threshold
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	77.2485	147	1223	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	77.2378	270	1223	95	below_threshold
Sphingomonas sanguinis	strain=NBRC 13937	GCA_001591005.1	33051	33051	suspected-type	True	77.157	279	1223	95	below_threshold
Sphingomonas aerophila	strain=DSM 100044	GCA_014199305.1	1344948	1344948	type	True	76.782	156	1223	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:32,035] [INFO] DFAST Taxonomy check result was written to GCF_013378075.1_ASM1337807v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:32,036] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:32,036] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:32,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3f586f4-0c92-4f0a-b1ba-01ce3cada5c9/dqc_reference/checkm_data
[2024-01-25 18:13:32,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:32,075] [INFO] Task started: CheckM
[2024-01-25 18:13:32,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013378075.1_ASM1337807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013378075.1_ASM1337807v1_genomic.fna/checkm_input GCF_013378075.1_ASM1337807v1_genomic.fna/checkm_result
[2024-01-25 18:14:00,976] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:00,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:00,996] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:00,996] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:00,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013378075.1_ASM1337807v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:00,996] [INFO] Task started: Blastn
[2024-01-25 18:14:00,996] [INFO] Running command: blastn -query GCF_013378075.1_ASM1337807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f586f4-0c92-4f0a-b1ba-01ce3cada5c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_013378075.1_ASM1337807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:02,657] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:02,670] [INFO] Selected 13 target genomes.
[2024-01-25 18:14:02,670] [INFO] Target genome list was writen to GCF_013378075.1_ASM1337807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:02,714] [INFO] Task started: fastANI
[2024-01-25 18:14:02,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg66ba44a4-7de9-45a7-b035-30bbfcdc8a93/GCF_013378075.1_ASM1337807v1_genomic.fna.gz --refList GCF_013378075.1_ASM1337807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013378075.1_ASM1337807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:11,754] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:11,762] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:11,763] [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_013378075.1	s__Parasphingopyxis algicola	100.0	1223	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014237875.1	s__Parasphingopyxis sp014237875	80.9254	637	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385775.1	s__Parasphingopyxis lamellibrachiae	80.8158	673	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001755.1	s__Parasphingopyxis sp013001755	80.0167	486	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013378055.1	s__Parasphingopyxis sp013378055	79.8126	608	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479515.1	s__Parasphingopyxis sp905479515	79.805	360	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	77.9313	317	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	77.7297	323	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_000016765.1	s__Rhizorhabdus wittichii	77.7132	383	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	77.6506	326	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641655.1	s__Alteriqipengyuania_A marina	77.5536	251	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	98.02	98.02	0.89	0.89	2	-
GCF_001423845.1	s__Sphingomonas sp001423845	77.4048	297	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827575.1	s__Alteriqipengyuania_A halimionae	77.3868	214	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:11,764] [INFO] GTDB search result was written to GCF_013378075.1_ASM1337807v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:11,764] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:11,767] [INFO] DFAST_QC result json was written to GCF_013378075.1_ASM1337807v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:11,768] [INFO] DFAST_QC completed!
[2024-01-25 18:14:11,768] [INFO] Total running time: 0h1m6s