[2024-01-24 13:46:10,772] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:10,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:10,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg661b8819-4530-4fcb-a9b0-f70354eaa394/dqc_reference
[2024-01-24 13:46:12,121] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:12,122] [INFO] Task started: Prodigal
[2024-01-24 13:46:12,122] [INFO] Running command: gunzip -c /var/lib/cwl/stga8b73219-fb69-4c6f-a76e-496e74fddd97/GCF_014705715.1_ASM1470571v1_genomic.fna.gz | prodigal -d GCF_014705715.1_ASM1470571v1_genomic.fna/cds.fna -a GCF_014705715.1_ASM1470571v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:21,983] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:21,983] [INFO] Task started: HMMsearch
[2024-01-24 13:46:21,983] [INFO] Running command: hmmsearch --tblout GCF_014705715.1_ASM1470571v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg661b8819-4530-4fcb-a9b0-f70354eaa394/dqc_reference/reference_markers.hmm GCF_014705715.1_ASM1470571v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:22,258] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:22,259] [INFO] Found 6/6 markers.
[2024-01-24 13:46:22,290] [INFO] Query marker FASTA was written to GCF_014705715.1_ASM1470571v1_genomic.fna/markers.fasta
[2024-01-24 13:46:22,290] [INFO] Task started: Blastn
[2024-01-24 13:46:22,290] [INFO] Running command: blastn -query GCF_014705715.1_ASM1470571v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg661b8819-4530-4fcb-a9b0-f70354eaa394/dqc_reference/reference_markers.fasta -out GCF_014705715.1_ASM1470571v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:23,259] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:23,262] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:23,262] [INFO] Target genome list was writen to GCF_014705715.1_ASM1470571v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:23,287] [INFO] Task started: fastANI
[2024-01-24 13:46:23,287] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b73219-fb69-4c6f-a76e-496e74fddd97/GCF_014705715.1_ASM1470571v1_genomic.fna.gz --refList GCF_014705715.1_ASM1470571v1_genomic.fna/target_genomes.txt --output GCF_014705715.1_ASM1470571v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:36,051] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:36,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg661b8819-4530-4fcb-a9b0-f70354eaa394/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:36,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg661b8819-4530-4fcb-a9b0-f70354eaa394/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:36,068] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:36,069] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:36,069] [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
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	100.0	1011	1012	95	conclusive
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.9363	477	1012	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.8994	473	1012	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.7678	403	1012	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	78.7209	406	1012	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.6483	401	1012	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.526	427	1012	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	78.5222	392	1012	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.4963	316	1012	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	78.442	401	1012	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	78.4312	405	1012	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.4121	438	1012	95	below_threshold
Erythrobacter insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	78.3582	366	1012	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	78.2347	254	1012	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.2346	311	1012	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	78.1811	272	1012	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.0631	288	1012	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.02	295	1012	95	below_threshold
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	77.7802	287	1012	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	77.6836	226	1012	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	77.3284	155	1012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:36,074] [INFO] DFAST Taxonomy check result was written to GCF_014705715.1_ASM1470571v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:36,075] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:36,075] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:36,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg661b8819-4530-4fcb-a9b0-f70354eaa394/dqc_reference/checkm_data
[2024-01-24 13:46:36,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:36,109] [INFO] Task started: CheckM
[2024-01-24 13:46:36,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014705715.1_ASM1470571v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014705715.1_ASM1470571v1_genomic.fna/checkm_input GCF_014705715.1_ASM1470571v1_genomic.fna/checkm_result
[2024-01-24 13:47:09,012] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:09,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:09,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:09,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:09,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014705715.1_ASM1470571v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:09,033] [INFO] Task started: Blastn
[2024-01-24 13:47:09,033] [INFO] Running command: blastn -query GCF_014705715.1_ASM1470571v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg661b8819-4530-4fcb-a9b0-f70354eaa394/dqc_reference/reference_markers_gtdb.fasta -out GCF_014705715.1_ASM1470571v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:10,678] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:10,683] [INFO] Selected 15 target genomes.
[2024-01-24 13:47:10,683] [INFO] Target genome list was writen to GCF_014705715.1_ASM1470571v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:10,722] [INFO] Task started: fastANI
[2024-01-24 13:47:10,723] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b73219-fb69-4c6f-a76e-496e74fddd97/GCF_014705715.1_ASM1470571v1_genomic.fna.gz --refList GCF_014705715.1_ASM1470571v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014705715.1_ASM1470571v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:19,939] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:19,952] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:19,953] [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_014705715.1	s__Erythrobacter sp014705715	100.0	1011	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019204025.1	s__Erythrobacter sp019204025	82.0085	724	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	79.754	556	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363635.1	s__Erythrobacter sp009363635	79.4406	520	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	78.9777	486	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264115.1	s__Erythrobacter sp003264115	78.9613	456	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719165.1	s__Erythrobacter litoralis	78.9268	478	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.7081	371	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706445.1	s__Erythrobacter sp002706445	78.6731	295	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	78.5793	399	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155425.1	s__Erythrobacter donghaensis	78.5162	428	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004095.1	s__Erythrobacter insulae	78.3582	366	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143235.1	s__Erythrobacter sanguineus	78.3571	444	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_019204045.1	s__Erythrobacter sp019204045	78.2868	318	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.2565	298	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:19,954] [INFO] GTDB search result was written to GCF_014705715.1_ASM1470571v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:19,955] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:19,959] [INFO] DFAST_QC result json was written to GCF_014705715.1_ASM1470571v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:19,960] [INFO] DFAST_QC completed!
[2024-01-24 13:47:19,960] [INFO] Total running time: 0h1m9s