[2024-01-24 11:26:38,934] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg2610af6e-5f86-49ec-ad4c-ecb4dcdf7d76/dqc_reference
[2024-01-24 11:26:40,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,320] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg04591af0-dd4e-4659-9ba0-94dba856e731/GCF_023805295.1_ASM2380529v1_genomic.fna.gz | prodigal -d GCF_023805295.1_ASM2380529v1_genomic.fna/cds.fna -a GCF_023805295.1_ASM2380529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:47,552] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:47,553] [INFO] Task started: HMMsearch
[2024-01-24 11:26:47,553] [INFO] Running command: hmmsearch --tblout GCF_023805295.1_ASM2380529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2610af6e-5f86-49ec-ad4c-ecb4dcdf7d76/dqc_reference/reference_markers.hmm GCF_023805295.1_ASM2380529v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:47,791] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:47,793] [INFO] Found 6/6 markers.
[2024-01-24 11:26:47,818] [INFO] Query marker FASTA was written to GCF_023805295.1_ASM2380529v1_genomic.fna/markers.fasta
[2024-01-24 11:26:47,818] [INFO] Task started: Blastn
[2024-01-24 11:26:47,819] [INFO] Running command: blastn -query GCF_023805295.1_ASM2380529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2610af6e-5f86-49ec-ad4c-ecb4dcdf7d76/dqc_reference/reference_markers.fasta -out GCF_023805295.1_ASM2380529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:48,712] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:48,715] [INFO] Selected 11 target genomes.
[2024-01-24 11:26:48,716] [INFO] Target genome list was writen to GCF_023805295.1_ASM2380529v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:48,727] [INFO] Task started: fastANI
[2024-01-24 11:26:48,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg04591af0-dd4e-4659-9ba0-94dba856e731/GCF_023805295.1_ASM2380529v1_genomic.fna.gz --refList GCF_023805295.1_ASM2380529v1_genomic.fna/target_genomes.txt --output GCF_023805295.1_ASM2380529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:55,091] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:55,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2610af6e-5f86-49ec-ad4c-ecb4dcdf7d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:55,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2610af6e-5f86-49ec-ad4c-ecb4dcdf7d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:55,105] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:55,106] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:55,106] [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
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	81.7265	533	776	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	81.6291	547	776	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	81.1143	493	776	95	below_threshold
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	79.6528	430	776	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	79.5531	384	776	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	78.4141	266	776	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	77.6906	257	776	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	77.5159	176	776	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	76.2506	68	776	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.1034	82	776	95	below_threshold
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	76.0936	61	776	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:55,107] [INFO] DFAST Taxonomy check result was written to GCF_023805295.1_ASM2380529v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:55,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:55,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:55,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2610af6e-5f86-49ec-ad4c-ecb4dcdf7d76/dqc_reference/checkm_data
[2024-01-24 11:26:55,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:55,133] [INFO] Task started: CheckM
[2024-01-24 11:26:55,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023805295.1_ASM2380529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023805295.1_ASM2380529v1_genomic.fna/checkm_input GCF_023805295.1_ASM2380529v1_genomic.fna/checkm_result
[2024-01-24 11:27:21,580] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:21,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:21,603] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:21,603] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:21,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023805295.1_ASM2380529v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:21,604] [INFO] Task started: Blastn
[2024-01-24 11:27:21,605] [INFO] Running command: blastn -query GCF_023805295.1_ASM2380529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2610af6e-5f86-49ec-ad4c-ecb4dcdf7d76/dqc_reference/reference_markers_gtdb.fasta -out GCF_023805295.1_ASM2380529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:23,315] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:23,319] [INFO] Selected 24 target genomes.
[2024-01-24 11:27:23,319] [INFO] Target genome list was writen to GCF_023805295.1_ASM2380529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:23,386] [INFO] Task started: fastANI
[2024-01-24 11:27:23,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg04591af0-dd4e-4659-9ba0-94dba856e731/GCF_023805295.1_ASM2380529v1_genomic.fna.gz --refList GCF_023805295.1_ASM2380529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023805295.1_ASM2380529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:36,703] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:36,729] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:36,729] [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_014195685.1	s__Sphingomicrobium lutaoense	79.5268	386	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001055.1	s__Sphingomicrobium sp004282935	79.4507	346	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	99.85	99.85	0.95	0.95	2	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	78.669	335	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396585.1	s__Sphingomicrobium rhizophilum	78.4141	266	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927725.1	s__Sphingomicrobium kaistense	78.2269	281	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003499275.1	s__Sphingomicrobium mesophila	78.226	290	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363895.1	s__Sphingomicrobium ginsengisoli	78.1547	273	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873795.1	s__Sphingomicrobium sp014873795	77.8304	189	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315525.1	s__Sphingobium yanoikuyae	77.7493	238	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCA_002457415.1	s__Sphingobium sp002457415	77.724	204	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	77.6813	252	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_003097155.1	s__Sphingomicrobium sp003097155	77.6471	226	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	77.6401	204	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_000383095.1	s__Sphingomonas_N sp000383095	77.605	214	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	77.5766	195	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584015.1	s__Alteraurantiacibacter xanthus	77.5066	179	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001556995.1	s__Erythrobacter sp001556995	77.4846	164	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	77.4218	182	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583725.1	s__Sphingomicrobium edaphi	77.3964	214	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	77.3575	193	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720115.1	s__Sphingorhabdus_B sp016720115	77.3436	144	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.85	99.81	0.95	0.95	3	-
GCF_000632225.1	s__Sphingomonas sp000632225	77.2525	231	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083475.1	s__Sphingomonas sp002083475	77.1311	190	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	75.7241	59	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:36,731] [INFO] GTDB search result was written to GCF_023805295.1_ASM2380529v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:36,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:36,735] [INFO] DFAST_QC result json was written to GCF_023805295.1_ASM2380529v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:36,736] [INFO] DFAST_QC completed!
[2024-01-24 11:27:36,736] [INFO] Total running time: 0h0m58s