[2024-01-24 11:20:34,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,399] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c4f2934-1863-4dc2-b198-8fea7431ef03/dqc_reference
[2024-01-24 11:20:35,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,613] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg02486b40-dac3-4137-9198-8ce72e23e197/GCF_019204025.1_ASM1920402v1_genomic.fna.gz | prodigal -d GCF_019204025.1_ASM1920402v1_genomic.fna/cds.fna -a GCF_019204025.1_ASM1920402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:45,381] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:45,382] [INFO] Task started: HMMsearch
[2024-01-24 11:20:45,382] [INFO] Running command: hmmsearch --tblout GCF_019204025.1_ASM1920402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c4f2934-1863-4dc2-b198-8fea7431ef03/dqc_reference/reference_markers.hmm GCF_019204025.1_ASM1920402v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:45,620] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:45,621] [INFO] Found 6/6 markers.
[2024-01-24 11:20:45,651] [INFO] Query marker FASTA was written to GCF_019204025.1_ASM1920402v1_genomic.fna/markers.fasta
[2024-01-24 11:20:45,652] [INFO] Task started: Blastn
[2024-01-24 11:20:45,652] [INFO] Running command: blastn -query GCF_019204025.1_ASM1920402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c4f2934-1863-4dc2-b198-8fea7431ef03/dqc_reference/reference_markers.fasta -out GCF_019204025.1_ASM1920402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:46,378] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:46,382] [INFO] Selected 26 target genomes.
[2024-01-24 11:20:46,383] [INFO] Target genome list was writen to GCF_019204025.1_ASM1920402v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:46,413] [INFO] Task started: fastANI
[2024-01-24 11:20:46,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg02486b40-dac3-4137-9198-8ce72e23e197/GCF_019204025.1_ASM1920402v1_genomic.fna.gz --refList GCF_019204025.1_ASM1920402v1_genomic.fna/target_genomes.txt --output GCF_019204025.1_ASM1920402v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:00,524] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:00,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c4f2934-1863-4dc2-b198-8fea7431ef03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:00,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c4f2934-1863-4dc2-b198-8fea7431ef03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:00,547] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:21:00,547] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:21:00,548] [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	82.0278	730	1048	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.1965	288	1048	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.6027	371	1048	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	78.5899	370	1048	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.4431	429	1048	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.4298	422	1048	95	below_threshold
Erythrobacter insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	78.322	356	1048	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.2334	288	1048	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.2056	353	1048	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.1995	260	1048	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.1491	234	1048	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	78.0945	342	1048	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	78.0929	337	1048	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.0777	292	1048	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	78.0711	344	1048	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	78.0283	284	1048	95	below_threshold
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	77.9874	277	1048	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	77.9518	245	1048	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	77.8708	248	1048	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.8704	247	1048	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	77.8685	234	1048	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.8087	221	1048	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.7316	283	1048	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	77.585	283	1048	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	77.2716	175	1048	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	76.9801	145	1048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:00,549] [INFO] DFAST Taxonomy check result was written to GCF_019204025.1_ASM1920402v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:00,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:00,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:00,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c4f2934-1863-4dc2-b198-8fea7431ef03/dqc_reference/checkm_data
[2024-01-24 11:21:00,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:00,581] [INFO] Task started: CheckM
[2024-01-24 11:21:00,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019204025.1_ASM1920402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019204025.1_ASM1920402v1_genomic.fna/checkm_input GCF_019204025.1_ASM1920402v1_genomic.fna/checkm_result
[2024-01-24 11:21:32,491] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:32,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:32,510] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:32,511] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:32,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019204025.1_ASM1920402v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:32,512] [INFO] Task started: Blastn
[2024-01-24 11:21:32,512] [INFO] Running command: blastn -query GCF_019204025.1_ASM1920402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c4f2934-1863-4dc2-b198-8fea7431ef03/dqc_reference/reference_markers_gtdb.fasta -out GCF_019204025.1_ASM1920402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:33,523] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:33,527] [INFO] Selected 17 target genomes.
[2024-01-24 11:21:33,527] [INFO] Target genome list was writen to GCF_019204025.1_ASM1920402v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:33,546] [INFO] Task started: fastANI
[2024-01-24 11:21:33,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg02486b40-dac3-4137-9198-8ce72e23e197/GCF_019204025.1_ASM1920402v1_genomic.fna.gz --refList GCF_019204025.1_ASM1920402v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019204025.1_ASM1920402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:44,468] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:44,484] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:44,484] [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
GCA_019204025.1	s__Erythrobacter sp019204025	100.0	1046	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014705715.1	s__Erythrobacter sp014705715	82.0278	730	1048	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	79.8926	537	1048	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	79.4401	531	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152865.1	s__Erythrobacter sp000152865	79.2577	447	1048	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	78.7607	345	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000714765.1	s__Erythrobacter sp000714765	78.7351	448	1048	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	78.5864	443	1048	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	78.5536	403	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	78.486	307	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_007004095.1	s__Erythrobacter insulae	78.3323	355	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.2462	317	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	78.1181	236	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828055.1	s__Erythrobacter ramosus	78.0924	342	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013822695.1	s__Erythrobacter sp013822695	77.7972	329	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	77.6145	216	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	77.555	265	1048	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 11:21:44,486] [INFO] GTDB search result was written to GCF_019204025.1_ASM1920402v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:44,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:44,490] [INFO] DFAST_QC result json was written to GCF_019204025.1_ASM1920402v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:44,490] [INFO] DFAST_QC completed!
[2024-01-24 11:21:44,491] [INFO] Total running time: 0h1m10s