[2024-01-24 12:15:04,032] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,035] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,035] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a0bd85c-3a02-4d3a-a5d2-32d5840345d2/dqc_reference
[2024-01-24 12:15:05,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,320] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg45c2a049-c5ab-45de-9dca-285ccd790dbe/GCF_024211255.1_ASM2421125v1_genomic.fna.gz | prodigal -d GCF_024211255.1_ASM2421125v1_genomic.fna/cds.fna -a GCF_024211255.1_ASM2421125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:15,358] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:15,359] [INFO] Task started: HMMsearch
[2024-01-24 12:15:15,359] [INFO] Running command: hmmsearch --tblout GCF_024211255.1_ASM2421125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a0bd85c-3a02-4d3a-a5d2-32d5840345d2/dqc_reference/reference_markers.hmm GCF_024211255.1_ASM2421125v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:15,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:15,596] [INFO] Found 6/6 markers.
[2024-01-24 12:15:15,637] [INFO] Query marker FASTA was written to GCF_024211255.1_ASM2421125v1_genomic.fna/markers.fasta
[2024-01-24 12:15:15,638] [INFO] Task started: Blastn
[2024-01-24 12:15:15,638] [INFO] Running command: blastn -query GCF_024211255.1_ASM2421125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a0bd85c-3a02-4d3a-a5d2-32d5840345d2/dqc_reference/reference_markers.fasta -out GCF_024211255.1_ASM2421125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:16,701] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:16,704] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:16,704] [INFO] Target genome list was writen to GCF_024211255.1_ASM2421125v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:16,709] [INFO] Task started: fastANI
[2024-01-24 12:15:16,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg45c2a049-c5ab-45de-9dca-285ccd790dbe/GCF_024211255.1_ASM2421125v1_genomic.fna.gz --refList GCF_024211255.1_ASM2421125v1_genomic.fna/target_genomes.txt --output GCF_024211255.1_ASM2421125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:28,848] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:28,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a0bd85c-3a02-4d3a-a5d2-32d5840345d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:28,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a0bd85c-3a02-4d3a-a5d2-32d5840345d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:28,860] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:28,860] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:28,860] [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 taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	87.1738	828	1167	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	85.7827	826	1167	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	85.7008	839	1167	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	85.6399	828	1167	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	85.6109	816	1167	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	85.5708	759	1167	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	81.4871	642	1167	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.9694	655	1167	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.8564	659	1167	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	80.7635	654	1167	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	80.2636	613	1167	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	80.1524	596	1167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,862] [INFO] DFAST Taxonomy check result was written to GCF_024211255.1_ASM2421125v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:28,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:28,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:28,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a0bd85c-3a02-4d3a-a5d2-32d5840345d2/dqc_reference/checkm_data
[2024-01-24 12:15:28,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:28,903] [INFO] Task started: CheckM
[2024-01-24 12:15:28,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024211255.1_ASM2421125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024211255.1_ASM2421125v1_genomic.fna/checkm_input GCF_024211255.1_ASM2421125v1_genomic.fna/checkm_result
[2024-01-24 12:16:00,013] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:00,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:00,030] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:00,031] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:00,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024211255.1_ASM2421125v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:00,032] [INFO] Task started: Blastn
[2024-01-24 12:16:00,032] [INFO] Running command: blastn -query GCF_024211255.1_ASM2421125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a0bd85c-3a02-4d3a-a5d2-32d5840345d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_024211255.1_ASM2421125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:01,958] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:01,963] [INFO] Selected 10 target genomes.
[2024-01-24 12:16:01,964] [INFO] Target genome list was writen to GCF_024211255.1_ASM2421125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:01,970] [INFO] Task started: fastANI
[2024-01-24 12:16:01,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg45c2a049-c5ab-45de-9dca-285ccd790dbe/GCF_024211255.1_ASM2421125v1_genomic.fna.gz --refList GCF_024211255.1_ASM2421125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024211255.1_ASM2421125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:11,775] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:11,785] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:11,786] [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_002292295.1	s__Sphingomonas sp002292295	87.4154	852	1167	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	87.1891	827	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_013409985.1	s__Sphingomonas melonis_A	86.8388	830	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632225.1	s__Sphingomonas sp000632225	86.0157	790	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010450875.1	s__Sphingomonas insulae	85.776	827	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014196115.1	s__Sphingomonas aquatilis	85.6126	830	1167	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	85.3216	825	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCF_003355005.1	s__Sphingomonas sp003355005	83.8132	772	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107325.1	s__Sphingomonas sp016107325	83.6374	783	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	82.0008	702	1167	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 12:16:11,787] [INFO] GTDB search result was written to GCF_024211255.1_ASM2421125v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:11,788] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:11,793] [INFO] DFAST_QC result json was written to GCF_024211255.1_ASM2421125v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:11,793] [INFO] DFAST_QC completed!
[2024-01-24 12:16:11,793] [INFO] Total running time: 0h1m8s