[2024-01-24 11:48:21,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,324] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg2edd54c4-25b1-434d-ad53-7d34628ac203/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaa20e6a-7f0d-47ef-9834-c76bb3050ace/GCF_016924655.1_ASM1692465v1_genomic.fna.gz | prodigal -d GCF_016924655.1_ASM1692465v1_genomic.fna/cds.fna -a GCF_016924655.1_ASM1692465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:32,642] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:32,643] [INFO] Task started: HMMsearch
[2024-01-24 11:48:32,643] [INFO] Running command: hmmsearch --tblout GCF_016924655.1_ASM1692465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2edd54c4-25b1-434d-ad53-7d34628ac203/dqc_reference/reference_markers.hmm GCF_016924655.1_ASM1692465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:32,883] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:32,884] [INFO] Found 6/6 markers.
[2024-01-24 11:48:32,913] [INFO] Query marker FASTA was written to GCF_016924655.1_ASM1692465v1_genomic.fna/markers.fasta
[2024-01-24 11:48:32,914] [INFO] Task started: Blastn
[2024-01-24 11:48:32,914] [INFO] Running command: blastn -query GCF_016924655.1_ASM1692465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2edd54c4-25b1-434d-ad53-7d34628ac203/dqc_reference/reference_markers.fasta -out GCF_016924655.1_ASM1692465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:33,826] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:33,830] [INFO] Selected 15 target genomes.
[2024-01-24 11:48:33,830] [INFO] Target genome list was writen to GCF_016924655.1_ASM1692465v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:33,872] [INFO] Task started: fastANI
[2024-01-24 11:48:33,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaa20e6a-7f0d-47ef-9834-c76bb3050ace/GCF_016924655.1_ASM1692465v1_genomic.fna.gz --refList GCF_016924655.1_ASM1692465v1_genomic.fna/target_genomes.txt --output GCF_016924655.1_ASM1692465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:41,588] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:41,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2edd54c4-25b1-434d-ad53-7d34628ac203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:41,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2edd54c4-25b1-434d-ad53-7d34628ac203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:41,605] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:48:41,606] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:48:41,606] [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 arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	100.0	916	916	95	conclusive
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	79.9212	429	916	95	below_threshold
Sphingomonas astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	79.7257	416	916	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	79.632	403	916	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	79.3681	399	916	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	78.996	282	916	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	78.802	322	916	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	78.6204	305	916	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	78.6196	342	916	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	78.5799	312	916	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_014396785.1	1045317	1045317	type	True	78.4865	315	916	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	78.2003	297	916	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.8804	270	916	95	below_threshold
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	77.6457	194	916	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	77.3919	205	916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:41,607] [INFO] DFAST Taxonomy check result was written to GCF_016924655.1_ASM1692465v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:41,608] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:41,608] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:41,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2edd54c4-25b1-434d-ad53-7d34628ac203/dqc_reference/checkm_data
[2024-01-24 11:48:41,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:41,639] [INFO] Task started: CheckM
[2024-01-24 11:48:41,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016924655.1_ASM1692465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016924655.1_ASM1692465v1_genomic.fna/checkm_input GCF_016924655.1_ASM1692465v1_genomic.fna/checkm_result
[2024-01-24 11:49:09,352] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:09,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:09,371] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:09,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:09,371] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016924655.1_ASM1692465v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:09,372] [INFO] Task started: Blastn
[2024-01-24 11:49:09,372] [INFO] Running command: blastn -query GCF_016924655.1_ASM1692465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2edd54c4-25b1-434d-ad53-7d34628ac203/dqc_reference/reference_markers_gtdb.fasta -out GCF_016924655.1_ASM1692465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:11,030] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:11,034] [INFO] Selected 13 target genomes.
[2024-01-24 11:49:11,034] [INFO] Target genome list was writen to GCF_016924655.1_ASM1692465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:11,044] [INFO] Task started: fastANI
[2024-01-24 11:49:11,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaa20e6a-7f0d-47ef-9834-c76bb3050ace/GCF_016924655.1_ASM1692465v1_genomic.fna.gz --refList GCF_016924655.1_ASM1692465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016924655.1_ASM1692465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:49:18,767] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:18,791] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:49:18,792] [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_016924655.1	s__Sphingomicrobium sp016924655	100.0	916	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014873375.1	s__Sphingomicrobium sp014873375	83.9154	700	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	80.4231	386	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806265.1	s__Sphingomicrobium sp902806265	80.1479	429	916	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	79.9602	426	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000711715.1	s__Sphingomicrobium astaxanthinifaciens	79.7634	413	916	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	79.6366	404	916	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	79.2972	405	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011300455.1	s__Sphingomicrobium piscis	78.996	282	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	78.9686	281	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873475.1	s__Sphingomicrobium sp014873475	78.8788	347	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489495.1	s__Sphingomicrobium daechungense	78.4585	286	916	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	78.3569	330	916	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:49:18,793] [INFO] GTDB search result was written to GCF_016924655.1_ASM1692465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:49:18,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:49:18,797] [INFO] DFAST_QC result json was written to GCF_016924655.1_ASM1692465v1_genomic.fna/dqc_result.json
[2024-01-24 11:49:18,797] [INFO] DFAST_QC completed!
[2024-01-24 11:49:18,798] [INFO] Total running time: 0h0m58s