[2024-01-24 14:19:15,871] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,874] [INFO] DQC Reference Directory: /var/lib/cwl/stgab83b312-e7e2-4811-9feb-b0727e794e15/dqc_reference
[2024-01-24 14:19:17,119] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:17,119] [INFO] Task started: Prodigal
[2024-01-24 14:19:17,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg69782569-79f4-48a3-9ce1-88c193fcf715/GCF_011302055.1_ASM1130205v1_genomic.fna.gz | prodigal -d GCF_011302055.1_ASM1130205v1_genomic.fna/cds.fna -a GCF_011302055.1_ASM1130205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:23,193] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:23,193] [INFO] Task started: HMMsearch
[2024-01-24 14:19:23,194] [INFO] Running command: hmmsearch --tblout GCF_011302055.1_ASM1130205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab83b312-e7e2-4811-9feb-b0727e794e15/dqc_reference/reference_markers.hmm GCF_011302055.1_ASM1130205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:23,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:23,467] [INFO] Found 6/6 markers.
[2024-01-24 14:19:23,493] [INFO] Query marker FASTA was written to GCF_011302055.1_ASM1130205v1_genomic.fna/markers.fasta
[2024-01-24 14:19:23,494] [INFO] Task started: Blastn
[2024-01-24 14:19:23,494] [INFO] Running command: blastn -query GCF_011302055.1_ASM1130205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab83b312-e7e2-4811-9feb-b0727e794e15/dqc_reference/reference_markers.fasta -out GCF_011302055.1_ASM1130205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:24,538] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:24,542] [INFO] Selected 17 target genomes.
[2024-01-24 14:19:24,543] [INFO] Target genome list was writen to GCF_011302055.1_ASM1130205v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:24,551] [INFO] Task started: fastANI
[2024-01-24 14:19:24,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg69782569-79f4-48a3-9ce1-88c193fcf715/GCF_011302055.1_ASM1130205v1_genomic.fna.gz --refList GCF_011302055.1_ASM1130205v1_genomic.fna/target_genomes.txt --output GCF_011302055.1_ASM1130205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:33,818] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:33,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab83b312-e7e2-4811-9feb-b0727e794e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:33,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab83b312-e7e2-4811-9feb-b0727e794e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:33,831] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:33,832] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:33,832] [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 sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	100.0	690	690	95	conclusive
Sphingomonas sabuli	strain=sand1-3	GCA_014352855.1	2764186	2764186	type	True	80.1717	422	690	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_014396785.1	1045317	1045317	type	True	79.6842	371	690	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	79.6724	373	690	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.2654	323	690	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	79.2398	329	690	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	79.1852	329	690	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.1425	346	690	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	79.113	341	690	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	79.069	341	690	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	79.0645	307	690	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.8111	211	690	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.618	208	690	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	77.5392	237	690	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	77.4504	201	690	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.4099	244	690	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.311	254	690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:33,834] [INFO] DFAST Taxonomy check result was written to GCF_011302055.1_ASM1130205v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:33,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:33,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:33,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab83b312-e7e2-4811-9feb-b0727e794e15/dqc_reference/checkm_data
[2024-01-24 14:19:33,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:33,858] [INFO] Task started: CheckM
[2024-01-24 14:19:33,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011302055.1_ASM1130205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011302055.1_ASM1130205v1_genomic.fna/checkm_input GCF_011302055.1_ASM1130205v1_genomic.fna/checkm_result
[2024-01-24 14:20:02,183] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:02,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:02,257] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:02,257] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:02,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011302055.1_ASM1130205v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:02,258] [INFO] Task started: Blastn
[2024-01-24 14:20:02,258] [INFO] Running command: blastn -query GCF_011302055.1_ASM1130205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab83b312-e7e2-4811-9feb-b0727e794e15/dqc_reference/reference_markers_gtdb.fasta -out GCF_011302055.1_ASM1130205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:04,765] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:04,768] [INFO] Selected 22 target genomes.
[2024-01-24 14:20:04,768] [INFO] Target genome list was writen to GCF_011302055.1_ASM1130205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:04,824] [INFO] Task started: fastANI
[2024-01-24 14:20:04,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg69782569-79f4-48a3-9ce1-88c193fcf715/GCF_011302055.1_ASM1130205v1_genomic.fna.gz --refList GCF_011302055.1_ASM1130205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011302055.1_ASM1130205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:19,998] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:20,026] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:20,026] [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_011302055.1	s__Sphingomicrobium sinipercae	100.0	690	690	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_014352855.1	s__Sphingomicrobium sp014352855	80.1717	422	690	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812805.1	s__Sphingomicrobium sp013812805	79.7083	325	690	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	79.4969	295	690	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	79.2638	354	690	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	79.1823	350	690	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	79.1727	356	690	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	79.1396	339	690	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	79.1345	348	690	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242355.1	s__Sphingomicrobium sp019242355	79.12	278	690	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	79.0645	307	690	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	79.0623	342	690	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	79.0346	323	690	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806275.1	s__Sphingomicrobium sp902806275	78.9995	251	690	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817375.1	s__Sphingomicrobium sp013817375	78.9283	302	690	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	78.6397	296	690	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	78.41	283	690	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	78.0255	288	690	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
GCA_002344055.1	s__Allosphingosinicella sp002344055	77.9613	237	690	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	77.516	237	690	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903642285.1	s__Sphingomonas sp903642285	77.3729	167	690	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	77.3068	256	690	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:20,028] [INFO] GTDB search result was written to GCF_011302055.1_ASM1130205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:20,040] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:20,049] [INFO] DFAST_QC result json was written to GCF_011302055.1_ASM1130205v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:20,049] [INFO] DFAST_QC completed!
[2024-01-24 14:20:20,049] [INFO] Total running time: 0h1m4s