[2023-06-29 17:08:57,381] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:08:57,383] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:08:57,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c6ce02d-f36b-4c65-9d90-0f6e831479da/dqc_reference
[2023-06-29 17:08:58,544] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:08:58,545] [INFO] Task started: Prodigal
[2023-06-29 17:08:58,545] [INFO] Running command: gunzip -c /var/lib/cwl/stg15e49d18-a3e8-494a-9b7a-f7ffff63246a/GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:09:04,007] [INFO] Task succeeded: Prodigal
[2023-06-29 17:09:04,008] [INFO] Task started: HMMsearch
[2023-06-29 17:09:04,008] [INFO] Running command: hmmsearch --tblout GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c6ce02d-f36b-4c65-9d90-0f6e831479da/dqc_reference/reference_markers.hmm GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:09:04,173] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:09:04,174] [INFO] Found 6/6 markers.
[2023-06-29 17:09:04,197] [INFO] Query marker FASTA was written to GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 17:09:04,197] [INFO] Task started: Blastn
[2023-06-29 17:09:04,197] [INFO] Running command: blastn -query GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c6ce02d-f36b-4c65-9d90-0f6e831479da/dqc_reference/reference_markers.fasta -out GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:09:05,005] [INFO] Task succeeded: Blastn
[2023-06-29 17:09:05,008] [INFO] Selected 14 target genomes.
[2023-06-29 17:09:05,009] [INFO] Target genome list was writen to GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 17:09:05,010] [INFO] Task started: fastANI
[2023-06-29 17:09:05,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg15e49d18-a3e8-494a-9b7a-f7ffff63246a/GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:09:12,149] [INFO] Task succeeded: fastANI
[2023-06-29 17:09:12,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c6ce02d-f36b-4c65-9d90-0f6e831479da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:09:12,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c6ce02d-f36b-4c65-9d90-0f6e831479da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:09:12,161] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:09:12,161] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 17:09:12,161] [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
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	84.7873	315	373	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	81.8223	271	373	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.7647	287	373	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	81.3716	261	373	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	81.2627	242	373	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	81.2028	254	373	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	81.0804	261	373	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	81.069	260	373	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	80.9928	264	373	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	80.8942	250	373	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	80.7688	251	373	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	80.2288	261	373	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	80.1194	219	373	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	79.874	202	373	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 17:09:12,163] [INFO] DFAST Taxonomy check result was written to GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 17:09:12,164] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:09:12,164] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:09:12,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c6ce02d-f36b-4c65-9d90-0f6e831479da/dqc_reference/checkm_data
[2023-06-29 17:09:12,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:09:12,190] [INFO] Task started: CheckM
[2023-06-29 17:09:12,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 17:09:33,573] [INFO] Task succeeded: CheckM
[2023-06-29 17:09:33,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 17:09:33,589] [INFO] ===== Completeness check finished =====
[2023-06-29 17:09:33,589] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:09:33,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 17:09:33,589] [INFO] Task started: Blastn
[2023-06-29 17:09:33,589] [INFO] Running command: blastn -query GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c6ce02d-f36b-4c65-9d90-0f6e831479da/dqc_reference/reference_markers_gtdb.fasta -out GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:09:35,122] [INFO] Task succeeded: Blastn
[2023-06-29 17:09:35,125] [INFO] Selected 10 target genomes.
[2023-06-29 17:09:35,125] [INFO] Target genome list was writen to GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:09:35,128] [INFO] Task started: fastANI
[2023-06-29 17:09:35,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg15e49d18-a3e8-494a-9b7a-f7ffff63246a/GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:09:40,043] [INFO] Task succeeded: fastANI
[2023-06-29 17:09:40,052] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 17:09:40,052] [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_009828015.1	s__Qipengyuania citrea	98.419	352	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	conclusive
GCA_016764075.1	s__Qipengyuania sp016764075	86.3829	288	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762005.1	s__Qipengyuania flava	84.7873	315	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_001542855.1	s__Qipengyuania sp001542855	82.8821	301	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_003355455.1	s__Qipengyuania aurea	82.1631	290	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_009827315.1	s__Qipengyuania gaetbuli	81.3554	261	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767595.1	s__Qipengyuania sp002895025	81.295	266	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_015529805.1	s__Qipengyuania soli	80.8187	249	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827325.1	s__Qipengyuania vulgaris	80.8027	224	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	80.5509	250	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 17:09:40,054] [INFO] GTDB search result was written to GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 17:09:40,054] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:09:40,057] [INFO] DFAST_QC result json was written to GCA_937901595.1_ERR599037_bin.22_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 17:09:40,057] [INFO] DFAST_QC completed!
[2023-06-29 17:09:40,058] [INFO] Total running time: 0h0m43s