[2024-01-24 11:43:42,229] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,242] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,242] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cbcdb99-f37b-4106-9012-5d3872b7e782/dqc_reference
[2024-01-24 11:43:43,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,631] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg21cf85b9-a1cf-41da-9e81-f4fa6898e68b/GCF_019204045.1_ASM1920404v1_genomic.fna.gz | prodigal -d GCF_019204045.1_ASM1920404v1_genomic.fna/cds.fna -a GCF_019204045.1_ASM1920404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:52,019] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:52,020] [INFO] Task started: HMMsearch
[2024-01-24 11:43:52,020] [INFO] Running command: hmmsearch --tblout GCF_019204045.1_ASM1920404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cbcdb99-f37b-4106-9012-5d3872b7e782/dqc_reference/reference_markers.hmm GCF_019204045.1_ASM1920404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:52,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:52,284] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg21cf85b9-a1cf-41da-9e81-f4fa6898e68b/GCF_019204045.1_ASM1920404v1_genomic.fna.gz]
[2024-01-24 11:43:52,319] [INFO] Query marker FASTA was written to GCF_019204045.1_ASM1920404v1_genomic.fna/markers.fasta
[2024-01-24 11:43:52,320] [INFO] Task started: Blastn
[2024-01-24 11:43:52,320] [INFO] Running command: blastn -query GCF_019204045.1_ASM1920404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cbcdb99-f37b-4106-9012-5d3872b7e782/dqc_reference/reference_markers.fasta -out GCF_019204045.1_ASM1920404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:53,133] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:53,135] [INFO] Selected 20 target genomes.
[2024-01-24 11:43:53,136] [INFO] Target genome list was writen to GCF_019204045.1_ASM1920404v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:53,177] [INFO] Task started: fastANI
[2024-01-24 11:43:53,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg21cf85b9-a1cf-41da-9e81-f4fa6898e68b/GCF_019204045.1_ASM1920404v1_genomic.fna.gz --refList GCF_019204045.1_ASM1920404v1_genomic.fna/target_genomes.txt --output GCF_019204045.1_ASM1920404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:05,065] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:05,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cbcdb99-f37b-4106-9012-5d3872b7e782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:05,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cbcdb99-f37b-4106-9012-5d3872b7e782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:05,080] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:05,080] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:05,081] [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 insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	79.823	456	860	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	78.4158	317	860	95	below_threshold
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	77.8665	246	860	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	77.3894	235	860	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	77.3414	237	860	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	77.2848	185	860	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.112	189	860	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	77.0959	164	860	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.0661	166	860	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.0582	149	860	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	76.9757	159	860	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	76.9316	154	860	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	76.9279	148	860	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	76.8729	174	860	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	76.8611	172	860	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	76.8164	157	860	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	76.4332	69	860	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	76.386	62	860	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	75.979	71	860	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:05,082] [INFO] DFAST Taxonomy check result was written to GCF_019204045.1_ASM1920404v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:05,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:05,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:05,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cbcdb99-f37b-4106-9012-5d3872b7e782/dqc_reference/checkm_data
[2024-01-24 11:44:05,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:05,110] [INFO] Task started: CheckM
[2024-01-24 11:44:05,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019204045.1_ASM1920404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019204045.1_ASM1920404v1_genomic.fna/checkm_input GCF_019204045.1_ASM1920404v1_genomic.fna/checkm_result
[2024-01-24 11:44:35,608] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:35,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:35,630] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:35,630] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:35,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019204045.1_ASM1920404v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:35,631] [INFO] Task started: Blastn
[2024-01-24 11:44:35,631] [INFO] Running command: blastn -query GCF_019204045.1_ASM1920404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cbcdb99-f37b-4106-9012-5d3872b7e782/dqc_reference/reference_markers_gtdb.fasta -out GCF_019204045.1_ASM1920404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:36,792] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:36,795] [INFO] Selected 18 target genomes.
[2024-01-24 11:44:36,795] [INFO] Target genome list was writen to GCF_019204045.1_ASM1920404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:36,809] [INFO] Task started: fastANI
[2024-01-24 11:44:36,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg21cf85b9-a1cf-41da-9e81-f4fa6898e68b/GCF_019204045.1_ASM1920404v1_genomic.fna.gz --refList GCF_019204045.1_ASM1920404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019204045.1_ASM1920404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:46,382] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:46,405] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:46,405] [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_019204045.1	s__Erythrobacter sp019204045	100.0	860	860	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_007004095.1	s__Erythrobacter insulae	79.8167	457	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705715.1	s__Erythrobacter sp014705715	78.4158	317	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019204025.1	s__Erythrobacter sp019204025	77.9946	288	860	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	77.8831	266	860	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	77.8807	304	860	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	77.7777	295	860	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	77.7045	268	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706445.1	s__Erythrobacter sp002706445	77.5367	194	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720465.1	s__Erythrobacter sp001720465	77.2831	217	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155685.1	s__Erythrobacter colymbi	77.112	189	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934325.1	s__Erythrobacter sp903934325	77.0989	208	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	76.9314	143	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	76.8416	131	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331285.1	s__Erythrobacter sp000331285	76.839	175	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724215.1	s__Erythrobacter sp001724215	76.8133	181	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	76.7376	125	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_018823325.1	s__Sphingobium sp018823325	75.8328	61	860	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	0.97	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:46,407] [INFO] GTDB search result was written to GCF_019204045.1_ASM1920404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:46,407] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:46,414] [INFO] DFAST_QC result json was written to GCF_019204045.1_ASM1920404v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:46,414] [INFO] DFAST_QC completed!
[2024-01-24 11:44:46,414] [INFO] Total running time: 0h1m4s