[2024-01-24 11:34:42,278] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:42,280] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:42,280] [INFO] DQC Reference Directory: /var/lib/cwl/stge12ec618-732b-4306-9ec2-daf4cc1b563f/dqc_reference
[2024-01-24 11:34:43,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:43,726] [INFO] Task started: Prodigal
[2024-01-24 11:34:43,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg476d4b3d-2d46-4a80-877b-d741978e0530/GCF_014636045.1_ASM1463604v1_genomic.fna.gz | prodigal -d GCF_014636045.1_ASM1463604v1_genomic.fna/cds.fna -a GCF_014636045.1_ASM1463604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:57,766] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:57,766] [INFO] Task started: HMMsearch
[2024-01-24 11:34:57,766] [INFO] Running command: hmmsearch --tblout GCF_014636045.1_ASM1463604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge12ec618-732b-4306-9ec2-daf4cc1b563f/dqc_reference/reference_markers.hmm GCF_014636045.1_ASM1463604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:58,070] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:58,071] [INFO] Found 6/6 markers.
[2024-01-24 11:34:58,113] [INFO] Query marker FASTA was written to GCF_014636045.1_ASM1463604v1_genomic.fna/markers.fasta
[2024-01-24 11:34:58,113] [INFO] Task started: Blastn
[2024-01-24 11:34:58,113] [INFO] Running command: blastn -query GCF_014636045.1_ASM1463604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12ec618-732b-4306-9ec2-daf4cc1b563f/dqc_reference/reference_markers.fasta -out GCF_014636045.1_ASM1463604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:58,989] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:58,991] [INFO] Selected 13 target genomes.
[2024-01-24 11:34:58,992] [INFO] Target genome list was writen to GCF_014636045.1_ASM1463604v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:58,993] [INFO] Task started: fastANI
[2024-01-24 11:34:58,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg476d4b3d-2d46-4a80-877b-d741978e0530/GCF_014636045.1_ASM1463604v1_genomic.fna.gz --refList GCF_014636045.1_ASM1463604v1_genomic.fna/target_genomes.txt --output GCF_014636045.1_ASM1463604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:13,006] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:13,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge12ec618-732b-4306-9ec2-daf4cc1b563f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:13,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge12ec618-732b-4306-9ec2-daf4cc1b563f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:13,026] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:13,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:13,027] [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 fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	100.0	1517	1520	95	conclusive
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	99.9993	1520	1520	95	conclusive
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	91.6272	952	1520	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	88.2535	867	1520	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	88.0577	948	1520	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	87.1379	1020	1520	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	86.4443	822	1520	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	83.7662	739	1520	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.3282	377	1520	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.2543	383	1520	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	78.1508	353	1520	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.1333	373	1520	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.8042	441	1520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:13,029] [INFO] DFAST Taxonomy check result was written to GCF_014636045.1_ASM1463604v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:13,030] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:13,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:13,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge12ec618-732b-4306-9ec2-daf4cc1b563f/dqc_reference/checkm_data
[2024-01-24 11:35:13,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:13,080] [INFO] Task started: CheckM
[2024-01-24 11:35:13,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636045.1_ASM1463604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636045.1_ASM1463604v1_genomic.fna/checkm_input GCF_014636045.1_ASM1463604v1_genomic.fna/checkm_result
[2024-01-24 11:35:55,998] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:55,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:56,014] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:56,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:56,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636045.1_ASM1463604v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:56,015] [INFO] Task started: Blastn
[2024-01-24 11:35:56,015] [INFO] Running command: blastn -query GCF_014636045.1_ASM1463604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12ec618-732b-4306-9ec2-daf4cc1b563f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636045.1_ASM1463604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:57,607] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:57,611] [INFO] Selected 10 target genomes.
[2024-01-24 11:35:57,611] [INFO] Target genome list was writen to GCF_014636045.1_ASM1463604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:57,615] [INFO] Task started: fastANI
[2024-01-24 11:35:57,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg476d4b3d-2d46-4a80-877b-d741978e0530/GCF_014636045.1_ASM1463604v1_genomic.fna.gz --refList GCF_014636045.1_ASM1463604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636045.1_ASM1463604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:09,004] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:09,020] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:09,020] [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_004152845.1	s__Sphingobium fuliginis	99.9993	1520	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	conclusive
GCA_000264945.2	s__Sphingobium indicum	91.5776	955	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_013375535.1	s__Sphingobium sp013375535	89.1987	999	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361945.1	s__Sphingobium barthaii_A	88.5325	1023	1520	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	88.0531	949	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_001005725.1	s__Sphingobium chungbukense	87.1028	1023	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_008692605.1	s__Sphingobium estronivorans	86.4499	822	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375555.1	s__Sphingobium sp013375555	86.2234	867	1520	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	85.5588	951	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412635.1	s__Sphingobium bisphenolivorans	83.92	812	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:09,022] [INFO] GTDB search result was written to GCF_014636045.1_ASM1463604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:09,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:09,028] [INFO] DFAST_QC result json was written to GCF_014636045.1_ASM1463604v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:09,029] [INFO] DFAST_QC completed!
[2024-01-24 11:36:09,029] [INFO] Total running time: 0h1m27s