[2024-01-24 13:26:26,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:26,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:26,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b581fb0-dc6c-4706-a0f1-d6d59971d5d5/dqc_reference
[2024-01-24 13:26:27,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:27,367] [INFO] Task started: Prodigal
[2024-01-24 13:26:27,368] [INFO] Running command: gunzip -c /var/lib/cwl/stg817fd73b-f9f5-4948-94a5-0791fb4b8649/GCF_003583725.1_ASM358372v1_genomic.fna.gz | prodigal -d GCF_003583725.1_ASM358372v1_genomic.fna/cds.fna -a GCF_003583725.1_ASM358372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:34,279] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:34,279] [INFO] Task started: HMMsearch
[2024-01-24 13:26:34,279] [INFO] Running command: hmmsearch --tblout GCF_003583725.1_ASM358372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b581fb0-dc6c-4706-a0f1-d6d59971d5d5/dqc_reference/reference_markers.hmm GCF_003583725.1_ASM358372v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:34,505] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:34,506] [INFO] Found 6/6 markers.
[2024-01-24 13:26:34,542] [INFO] Query marker FASTA was written to GCF_003583725.1_ASM358372v1_genomic.fna/markers.fasta
[2024-01-24 13:26:34,542] [INFO] Task started: Blastn
[2024-01-24 13:26:34,542] [INFO] Running command: blastn -query GCF_003583725.1_ASM358372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b581fb0-dc6c-4706-a0f1-d6d59971d5d5/dqc_reference/reference_markers.fasta -out GCF_003583725.1_ASM358372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:35,356] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:35,360] [INFO] Selected 21 target genomes.
[2024-01-24 13:26:35,361] [INFO] Target genome list was writen to GCF_003583725.1_ASM358372v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:35,451] [INFO] Task started: fastANI
[2024-01-24 13:26:35,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg817fd73b-f9f5-4948-94a5-0791fb4b8649/GCF_003583725.1_ASM358372v1_genomic.fna.gz --refList GCF_003583725.1_ASM358372v1_genomic.fna/target_genomes.txt --output GCF_003583725.1_ASM358372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:45,974] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:45,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b581fb0-dc6c-4706-a0f1-d6d59971d5d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:45,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b581fb0-dc6c-4706-a0f1-d6d59971d5d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:45,993] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:45,993] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:45,993] [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 edaphi	strain=DAC4	GCA_003583725.1	2315689	2315689	type	True	100.0	788	789	95	conclusive
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	79.5935	385	789	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.2218	337	789	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	79.0297	366	789	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	78.4181	290	789	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	78.3231	220	789	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	78.2756	253	789	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	78.2381	250	789	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.2256	268	789	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.1765	263	789	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	77.8602	198	789	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	77.8364	215	789	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	77.8276	218	789	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.3925	178	789	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.3698	168	789	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	77.326	152	789	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.1858	101	789	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.1018	170	789	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	76.1869	58	789	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:45,995] [INFO] DFAST Taxonomy check result was written to GCF_003583725.1_ASM358372v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:45,996] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:45,996] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:45,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b581fb0-dc6c-4706-a0f1-d6d59971d5d5/dqc_reference/checkm_data
[2024-01-24 13:26:45,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:46,030] [INFO] Task started: CheckM
[2024-01-24 13:26:46,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003583725.1_ASM358372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003583725.1_ASM358372v1_genomic.fna/checkm_input GCF_003583725.1_ASM358372v1_genomic.fna/checkm_result
[2024-01-24 13:27:11,863] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:11,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:11,885] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:11,885] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:11,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003583725.1_ASM358372v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:11,886] [INFO] Task started: Blastn
[2024-01-24 13:27:11,886] [INFO] Running command: blastn -query GCF_003583725.1_ASM358372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b581fb0-dc6c-4706-a0f1-d6d59971d5d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003583725.1_ASM358372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:13,363] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:13,368] [INFO] Selected 17 target genomes.
[2024-01-24 13:27:13,368] [INFO] Target genome list was writen to GCF_003583725.1_ASM358372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:13,738] [INFO] Task started: fastANI
[2024-01-24 13:27:13,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg817fd73b-f9f5-4948-94a5-0791fb4b8649/GCF_003583725.1_ASM358372v1_genomic.fna.gz --refList GCF_003583725.1_ASM358372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003583725.1_ASM358372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:21,993] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:22,010] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:22,010] [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_003583725.1	s__Sphingomicrobium edaphi	100.0	788	789	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_000585415.1	s__Sphingomicrobium jaspsi	79.5801	386	789	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	79.2218	337	789	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	79.0297	366	789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816785.1	s__Sphingomicrobium sp013816785	78.566	313	789	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	78.4043	291	789	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	78.3613	248	789	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	78.3162	221	789	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	78.2756	253	789	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	78.2535	266	789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011301715.1	s__Sphingomicrobium sp011301715	78.173	265	789	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	77.8526	193	789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	77.7899	155	789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_002117915.1	s__Sphingomonas sp002117915	77.4789	157	789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591025.1	s__Sphingomonas soli	77.3452	151	789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550065.1	s__Sphingomonas caeni	77.3415	148	789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	77.3394	211	789	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 13:27:22,012] [INFO] GTDB search result was written to GCF_003583725.1_ASM358372v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:22,013] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:22,017] [INFO] DFAST_QC result json was written to GCF_003583725.1_ASM358372v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:22,017] [INFO] DFAST_QC completed!
[2024-01-24 13:27:22,017] [INFO] Total running time: 0h0m56s