[2024-01-24 12:48:20,266] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:20,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:20,269] [INFO] DQC Reference Directory: /var/lib/cwl/stgb226731d-0866-4605-8dde-4232df7b7518/dqc_reference
[2024-01-24 12:48:21,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:21,468] [INFO] Task started: Prodigal
[2024-01-24 12:48:21,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a7e3c8e-7ea0-4c1a-a859-ea32414d6189/GCF_030160555.1_ASM3016055v1_genomic.fna.gz | prodigal -d GCF_030160555.1_ASM3016055v1_genomic.fna/cds.fna -a GCF_030160555.1_ASM3016055v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:28,033] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:28,034] [INFO] Task started: HMMsearch
[2024-01-24 12:48:28,034] [INFO] Running command: hmmsearch --tblout GCF_030160555.1_ASM3016055v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb226731d-0866-4605-8dde-4232df7b7518/dqc_reference/reference_markers.hmm GCF_030160555.1_ASM3016055v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:28,244] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:28,246] [INFO] Found 6/6 markers.
[2024-01-24 12:48:28,274] [INFO] Query marker FASTA was written to GCF_030160555.1_ASM3016055v1_genomic.fna/markers.fasta
[2024-01-24 12:48:28,274] [INFO] Task started: Blastn
[2024-01-24 12:48:28,274] [INFO] Running command: blastn -query GCF_030160555.1_ASM3016055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb226731d-0866-4605-8dde-4232df7b7518/dqc_reference/reference_markers.fasta -out GCF_030160555.1_ASM3016055v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:29,298] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:29,303] [INFO] Selected 15 target genomes.
[2024-01-24 12:48:29,303] [INFO] Target genome list was writen to GCF_030160555.1_ASM3016055v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:29,320] [INFO] Task started: fastANI
[2024-01-24 12:48:29,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a7e3c8e-7ea0-4c1a-a859-ea32414d6189/GCF_030160555.1_ASM3016055v1_genomic.fna.gz --refList GCF_030160555.1_ASM3016055v1_genomic.fna/target_genomes.txt --output GCF_030160555.1_ASM3016055v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:38,588] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:38,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb226731d-0866-4605-8dde-4232df7b7518/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:38,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb226731d-0866-4605-8dde-4232df7b7518/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:38,602] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:38,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:38,602] [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 astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	99.9965	822	824	95	conclusive
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	83.3569	615	824	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	81.7708	576	824	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	80.5898	474	824	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	80.09	435	824	95	below_threshold
Sphingomonas arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	79.7142	422	824	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	79.3611	393	824	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	79.3603	359	824	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	79.2079	339	824	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	78.4938	353	824	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.2946	342	824	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.1659	305	824	95	below_threshold
Sphingomonas guangdongensis	strain=CGMCC 1.12672	GCA_900199185.1	1141890	1141890	type	True	78.1434	292	824	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.928	313	824	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.927	325	824	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:38,604] [INFO] DFAST Taxonomy check result was written to GCF_030160555.1_ASM3016055v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:38,604] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:38,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:38,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb226731d-0866-4605-8dde-4232df7b7518/dqc_reference/checkm_data
[2024-01-24 12:48:38,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:38,633] [INFO] Task started: CheckM
[2024-01-24 12:48:38,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160555.1_ASM3016055v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160555.1_ASM3016055v1_genomic.fna/checkm_input GCF_030160555.1_ASM3016055v1_genomic.fna/checkm_result
[2024-01-24 12:49:03,155] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:03,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:03,174] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:03,175] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:03,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160555.1_ASM3016055v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:03,176] [INFO] Task started: Blastn
[2024-01-24 12:49:03,176] [INFO] Running command: blastn -query GCF_030160555.1_ASM3016055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb226731d-0866-4605-8dde-4232df7b7518/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160555.1_ASM3016055v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:05,190] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:05,195] [INFO] Selected 14 target genomes.
[2024-01-24 12:49:05,195] [INFO] Target genome list was writen to GCF_030160555.1_ASM3016055v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:05,211] [INFO] Task started: fastANI
[2024-01-24 12:49:05,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a7e3c8e-7ea0-4c1a-a859-ea32414d6189/GCF_030160555.1_ASM3016055v1_genomic.fna.gz --refList GCF_030160555.1_ASM3016055v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160555.1_ASM3016055v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:13,892] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:13,905] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:13,906] [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_000711715.1	s__Sphingomicrobium astaxanthinifaciens	99.9965	822	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011927725.1	s__Sphingomicrobium kaistense	83.3713	614	824	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	81.806	572	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	80.5733	476	824	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	80.1984	394	824	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	79.7357	315	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924655.1	s__Sphingomicrobium sp016924655	79.7015	423	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873375.1	s__Sphingomicrobium sp014873375	79.4249	396	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009720245.1	s__Sphingomicrobium sp009720245	79.2076	339	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	78.4717	355	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_014641735.1	s__Sphingomonas metalli	78.3427	336	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241485.1	s__Sphingomonas sp000241485	78.2406	329	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199185.1	s__Sphingomonas guangdongensis	78.1678	290	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083435.1	s__Sphingomonas sp002083435	77.5862	285	824	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 12:49:13,907] [INFO] GTDB search result was written to GCF_030160555.1_ASM3016055v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:13,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:13,911] [INFO] DFAST_QC result json was written to GCF_030160555.1_ASM3016055v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:13,912] [INFO] DFAST_QC completed!
[2024-01-24 12:49:13,912] [INFO] Total running time: 0h0m54s