[2024-01-24 12:09:02,779] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:02,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:02,781] [INFO] DQC Reference Directory: /var/lib/cwl/stg7383ea1a-6a84-4111-b6f2-a57f26af1433/dqc_reference
[2024-01-24 12:09:03,992] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:03,993] [INFO] Task started: Prodigal
[2024-01-24 12:09:03,993] [INFO] Running command: gunzip -c /var/lib/cwl/stge0ad0cca-a182-4e0f-8c21-d1f1a0bacb3d/GCF_026157085.1_ASM2615708v1_genomic.fna.gz | prodigal -d GCF_026157085.1_ASM2615708v1_genomic.fna/cds.fna -a GCF_026157085.1_ASM2615708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:11,663] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:11,663] [INFO] Task started: HMMsearch
[2024-01-24 12:09:11,663] [INFO] Running command: hmmsearch --tblout GCF_026157085.1_ASM2615708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7383ea1a-6a84-4111-b6f2-a57f26af1433/dqc_reference/reference_markers.hmm GCF_026157085.1_ASM2615708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:11,909] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:11,911] [INFO] Found 6/6 markers.
[2024-01-24 12:09:11,939] [INFO] Query marker FASTA was written to GCF_026157085.1_ASM2615708v1_genomic.fna/markers.fasta
[2024-01-24 12:09:11,939] [INFO] Task started: Blastn
[2024-01-24 12:09:11,939] [INFO] Running command: blastn -query GCF_026157085.1_ASM2615708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7383ea1a-6a84-4111-b6f2-a57f26af1433/dqc_reference/reference_markers.fasta -out GCF_026157085.1_ASM2615708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:12,893] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:12,896] [INFO] Selected 10 target genomes.
[2024-01-24 12:09:12,897] [INFO] Target genome list was writen to GCF_026157085.1_ASM2615708v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:12,904] [INFO] Task started: fastANI
[2024-01-24 12:09:12,904] [INFO] Running command: fastANI --query /var/lib/cwl/stge0ad0cca-a182-4e0f-8c21-d1f1a0bacb3d/GCF_026157085.1_ASM2615708v1_genomic.fna.gz --refList GCF_026157085.1_ASM2615708v1_genomic.fna/target_genomes.txt --output GCF_026157085.1_ASM2615708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:18,683] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:18,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7383ea1a-6a84-4111-b6f2-a57f26af1433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:18,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7383ea1a-6a84-4111-b6f2-a57f26af1433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:18,695] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:09:18,695] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:09:18,695] [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	86.4449	646	852	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	86.3449	657	852	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	84.9784	608	852	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	79.846	415	852	95	below_threshold
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	79.7171	439	852	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	78.6509	292	852	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	78.5342	326	852	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.5122	300	852	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	77.7646	280	852	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.5939	239	852	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:18,697] [INFO] DFAST Taxonomy check result was written to GCF_026157085.1_ASM2615708v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:18,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:18,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:18,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7383ea1a-6a84-4111-b6f2-a57f26af1433/dqc_reference/checkm_data
[2024-01-24 12:09:18,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:18,724] [INFO] Task started: CheckM
[2024-01-24 12:09:18,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026157085.1_ASM2615708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026157085.1_ASM2615708v1_genomic.fna/checkm_input GCF_026157085.1_ASM2615708v1_genomic.fna/checkm_result
[2024-01-24 12:09:45,363] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:45,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:45,385] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:45,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:45,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026157085.1_ASM2615708v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:45,386] [INFO] Task started: Blastn
[2024-01-24 12:09:45,386] [INFO] Running command: blastn -query GCF_026157085.1_ASM2615708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7383ea1a-6a84-4111-b6f2-a57f26af1433/dqc_reference/reference_markers_gtdb.fasta -out GCF_026157085.1_ASM2615708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:47,202] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:47,205] [INFO] Selected 25 target genomes.
[2024-01-24 12:09:47,205] [INFO] Target genome list was writen to GCF_026157085.1_ASM2615708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:47,223] [INFO] Task started: fastANI
[2024-01-24 12:09:47,223] [INFO] Running command: fastANI --query /var/lib/cwl/stge0ad0cca-a182-4e0f-8c21-d1f1a0bacb3d/GCF_026157085.1_ASM2615708v1_genomic.fna.gz --refList GCF_026157085.1_ASM2615708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026157085.1_ASM2615708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:00,245] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:00,275] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:10:00,276] [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	79.846	415	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	79.0756	353	852	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	78.9744	337	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	99.85	99.85	0.95	0.95	2	-
GCF_000711715.1	s__Sphingomicrobium astaxanthinifaciens	78.7793	354	852	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	78.5915	340	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003499275.1	s__Sphingomicrobium mesophila	78.5459	325	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	78.5194	299	852	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	78.4479	306	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011302055.1	s__Sphingomicrobium sinipercae	78.1266	237	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097155.1	s__Sphingomicrobium sp003097155	78.0362	256	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007998985.1	s__Sphingomicrobium xanthus	77.9882	251	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632225.1	s__Sphingomonas sp000632225	77.9727	271	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016025255.1	s__Allosphingosinicella sp016025255	77.9555	235	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720245.1	s__Sphingomicrobium sp009720245	77.8912	228	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247755.1	s__Sphingomicrobium sp019247755	77.833	164	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018682675.1	s__Sphingopyxis soli	77.8213	251	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	77.8089	226	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005865.1	s__Rhizorhabdus crocodyli	77.8065	242	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314325.1	s__Sphingopyxis macrogoltabida	77.7963	276	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000712135.1	s__Sphingomonas sp000712135	77.7845	253	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489515.1	s__Sphingomicrobium sediminicola	77.7812	217	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363635.1	s__Erythrobacter sp009363635	77.5517	152	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828055.1	s__Erythrobacter ramosus	77.515	185	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017815135.1	s__Jiella sp017815135	76.584	107	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:10:00,278] [INFO] GTDB search result was written to GCF_026157085.1_ASM2615708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:00,278] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:00,285] [INFO] DFAST_QC result json was written to GCF_026157085.1_ASM2615708v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:00,285] [INFO] DFAST_QC completed!
[2024-01-24 12:10:00,285] [INFO] Total running time: 0h0m58s