[2024-01-24 11:20:19,440] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,442] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg88a9a4c3-a884-4e60-8c1a-513ad696d128/dqc_reference
[2024-01-24 11:20:20,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,655] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg9558cfdd-c74c-4dec-9e0b-07422ad9500a/GCF_003970925.1_ASM397092v1_genomic.fna.gz | prodigal -d GCF_003970925.1_ASM397092v1_genomic.fna/cds.fna -a GCF_003970925.1_ASM397092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:29,290] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:29,291] [INFO] Task started: HMMsearch
[2024-01-24 11:20:29,291] [INFO] Running command: hmmsearch --tblout GCF_003970925.1_ASM397092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88a9a4c3-a884-4e60-8c1a-513ad696d128/dqc_reference/reference_markers.hmm GCF_003970925.1_ASM397092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:29,591] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:29,593] [INFO] Found 6/6 markers.
[2024-01-24 11:20:29,624] [INFO] Query marker FASTA was written to GCF_003970925.1_ASM397092v1_genomic.fna/markers.fasta
[2024-01-24 11:20:29,624] [INFO] Task started: Blastn
[2024-01-24 11:20:29,624] [INFO] Running command: blastn -query GCF_003970925.1_ASM397092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88a9a4c3-a884-4e60-8c1a-513ad696d128/dqc_reference/reference_markers.fasta -out GCF_003970925.1_ASM397092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:30,624] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:30,627] [INFO] Selected 17 target genomes.
[2024-01-24 11:20:30,627] [INFO] Target genome list was writen to GCF_003970925.1_ASM397092v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:30,659] [INFO] Task started: fastANI
[2024-01-24 11:20:30,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg9558cfdd-c74c-4dec-9e0b-07422ad9500a/GCF_003970925.1_ASM397092v1_genomic.fna.gz --refList GCF_003970925.1_ASM397092v1_genomic.fna/target_genomes.txt --output GCF_003970925.1_ASM397092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:41,126] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:41,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88a9a4c3-a884-4e60-8c1a-513ad696d128/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:41,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88a9a4c3-a884-4e60-8c1a-513ad696d128/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:41,153] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:41,153] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:41,153] [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 ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	100.0	1071	1071	95	conclusive
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	80.8059	522	1071	95	below_threshold
Sphingomonas astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	80.5183	497	1071	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	80.164	426	1071	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	80.0106	475	1071	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.3943	392	1071	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	79.3326	370	1071	95	below_threshold
Sphingomonas arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	79.2392	412	1071	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	79.1226	369	1071	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	79.0673	358	1071	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	79.0267	355	1071	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.9993	431	1071	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.6767	448	1071	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.6728	448	1071	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.6137	394	1071	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.4793	360	1071	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.926	344	1071	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:41,155] [INFO] DFAST Taxonomy check result was written to GCF_003970925.1_ASM397092v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:41,156] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:41,156] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:41,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88a9a4c3-a884-4e60-8c1a-513ad696d128/dqc_reference/checkm_data
[2024-01-24 11:20:41,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:41,194] [INFO] Task started: CheckM
[2024-01-24 11:20:41,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970925.1_ASM397092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970925.1_ASM397092v1_genomic.fna/checkm_input GCF_003970925.1_ASM397092v1_genomic.fna/checkm_result
[2024-01-24 11:21:11,017] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:11,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:11,038] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:11,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:11,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970925.1_ASM397092v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:11,039] [INFO] Task started: Blastn
[2024-01-24 11:21:11,040] [INFO] Running command: blastn -query GCF_003970925.1_ASM397092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88a9a4c3-a884-4e60-8c1a-513ad696d128/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970925.1_ASM397092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:13,086] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:13,090] [INFO] Selected 16 target genomes.
[2024-01-24 11:21:13,090] [INFO] Target genome list was writen to GCF_003970925.1_ASM397092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:13,105] [INFO] Task started: fastANI
[2024-01-24 11:21:13,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg9558cfdd-c74c-4dec-9e0b-07422ad9500a/GCF_003970925.1_ASM397092v1_genomic.fna.gz --refList GCF_003970925.1_ASM397092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970925.1_ASM397092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:22,320] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:22,333] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:22,333] [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_003970925.1	s__Sphingomicrobium sp003970925	100.0	1071	1071	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_009363895.1	s__Sphingomicrobium ginsengisoli	80.8274	521	1071	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	80.5546	494	1071	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	80.178	426	1071	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	80.0173	474	1071	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	79.9968	398	1071	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	79.7756	399	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812825.1	s__Sphingomicrobium sp013812825	79.6527	395	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620665.1	s__Sphingomicrobium sp000620665	79.3905	404	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873375.1	s__Sphingomicrobium sp014873375	79.2443	386	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016924655.1	s__Sphingomicrobium sp016924655	79.2392	412	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011302055.1	s__Sphingomicrobium sinipercae	79.0678	358	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873795.1	s__Sphingomicrobium sp014873795	78.9855	322	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	78.7997	331	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	78.4567	362	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304635.1	s__Sphingomonas sp017304635	78.0421	355	1071	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 11:21:22,335] [INFO] GTDB search result was written to GCF_003970925.1_ASM397092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:22,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:22,339] [INFO] DFAST_QC result json was written to GCF_003970925.1_ASM397092v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:22,339] [INFO] DFAST_QC completed!
[2024-01-24 11:21:22,339] [INFO] Total running time: 0h1m3s