[2024-01-24 12:53:57,017] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:57,019] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:57,020] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f712891-515b-4746-99e9-ccb416fe7907/dqc_reference
[2024-01-24 12:53:58,458] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,459] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dfd461d-88d6-49d3-89b6-53ad43c26f01/GCF_007004095.1_ASM700409v1_genomic.fna.gz | prodigal -d GCF_007004095.1_ASM700409v1_genomic.fna/cds.fna -a GCF_007004095.1_ASM700409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:07,904] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:07,904] [INFO] Task started: HMMsearch
[2024-01-24 12:54:07,904] [INFO] Running command: hmmsearch --tblout GCF_007004095.1_ASM700409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f712891-515b-4746-99e9-ccb416fe7907/dqc_reference/reference_markers.hmm GCF_007004095.1_ASM700409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:08,148] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:08,151] [INFO] Found 6/6 markers.
[2024-01-24 12:54:08,184] [INFO] Query marker FASTA was written to GCF_007004095.1_ASM700409v1_genomic.fna/markers.fasta
[2024-01-24 12:54:08,185] [INFO] Task started: Blastn
[2024-01-24 12:54:08,185] [INFO] Running command: blastn -query GCF_007004095.1_ASM700409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f712891-515b-4746-99e9-ccb416fe7907/dqc_reference/reference_markers.fasta -out GCF_007004095.1_ASM700409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:08,931] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:08,935] [INFO] Selected 22 target genomes.
[2024-01-24 12:54:08,935] [INFO] Target genome list was writen to GCF_007004095.1_ASM700409v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:08,953] [INFO] Task started: fastANI
[2024-01-24 12:54:08,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dfd461d-88d6-49d3-89b6-53ad43c26f01/GCF_007004095.1_ASM700409v1_genomic.fna.gz --refList GCF_007004095.1_ASM700409v1_genomic.fna/target_genomes.txt --output GCF_007004095.1_ASM700409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:19,234] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:19,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f712891-515b-4746-99e9-ccb416fe7907/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:19,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f712891-515b-4746-99e9-ccb416fe7907/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:19,252] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:19,252] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:19,252] [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	100.0	994	994	95	conclusive
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	78.2889	374	994	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	77.5299	243	994	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.52	146	994	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	77.4807	247	994	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	77.4671	208	994	95	below_threshold
Qipengyuania psychrotolerans	strain=1XM2-8	GCA_019711355.1	2867238	2867238	type	True	77.4662	162	994	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	77.453	303	994	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	77.4441	296	994	95	below_threshold
Altererythrobacter ishigakiensis	strain=ATCC BAA-2084	GCA_007830695.1	476157	476157	type	True	77.3796	177	994	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.3715	169	994	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.3615	160	994	95	below_threshold
Altererythrobacter ishigakiensis	strain=NBRC 107699	GCA_001663155.1	476157	476157	type	True	77.3243	175	994	95	below_threshold
Altericroceibacterium endophyticum	strain=LMG 29518	GCA_009827595.1	1808508	1808508	type	True	77.269	125	994	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	77.256	144	994	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.0114	236	994	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	76.9934	168	994	95	below_threshold
Tsuneonella flava	strain=MS1-4	GCA_002870965.1	2055955	2055955	type	True	76.9797	148	994	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	76.92	153	994	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	76.9052	142	994	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.7641	124	994	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	76.6779	188	994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:19,254] [INFO] DFAST Taxonomy check result was written to GCF_007004095.1_ASM700409v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:19,255] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:19,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:19,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f712891-515b-4746-99e9-ccb416fe7907/dqc_reference/checkm_data
[2024-01-24 12:54:19,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:19,286] [INFO] Task started: CheckM
[2024-01-24 12:54:19,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007004095.1_ASM700409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007004095.1_ASM700409v1_genomic.fna/checkm_input GCF_007004095.1_ASM700409v1_genomic.fna/checkm_result
[2024-01-24 12:54:50,687] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:50,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:50,712] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:50,712] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:50,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007004095.1_ASM700409v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:50,713] [INFO] Task started: Blastn
[2024-01-24 12:54:50,713] [INFO] Running command: blastn -query GCF_007004095.1_ASM700409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f712891-515b-4746-99e9-ccb416fe7907/dqc_reference/reference_markers_gtdb.fasta -out GCF_007004095.1_ASM700409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:51,895] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:51,898] [INFO] Selected 17 target genomes.
[2024-01-24 12:54:51,898] [INFO] Target genome list was writen to GCF_007004095.1_ASM700409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:51,927] [INFO] Task started: fastANI
[2024-01-24 12:54:51,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dfd461d-88d6-49d3-89b6-53ad43c26f01/GCF_007004095.1_ASM700409v1_genomic.fna.gz --refList GCF_007004095.1_ASM700409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007004095.1_ASM700409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:01,345] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:01,359] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:01,359] [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_007004095.1	s__Erythrobacter insulae	100.0	994	994	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_019204045.1	s__Erythrobacter sp019204045	79.7515	452	994	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	78.2792	375	994	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	78.1999	359	994	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	78.0901	367	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900149685.1	s__Erythrobacter sp900149685	77.9971	287	994	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	77.9507	295	994	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	77.8892	309	994	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	77.7201	353	994	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	77.5674	210	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744895.1	s__Erythrobacter sp000744895	77.5283	286	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542875.1	s__Erythrobacter sp001542875	77.5231	252	994	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	77.4528	303	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002952215.1	s__Erythrobacter sp002952215	77.3338	234	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855495.1	s__Erythrobacter sp002855495	77.3045	246	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905735.1	s__Erythrobacter sp009905735	77.2268	255	994	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	77.0875	237	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:01,361] [INFO] GTDB search result was written to GCF_007004095.1_ASM700409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:01,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:01,366] [INFO] DFAST_QC result json was written to GCF_007004095.1_ASM700409v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:01,366] [INFO] DFAST_QC completed!
[2024-01-24 12:55:01,366] [INFO] Total running time: 0h1m4s