[2024-01-24 14:47:05,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:05,845] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:05,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg5af8d0a2-e111-4d8e-bbf5-995f72537cc1/dqc_reference
[2024-01-24 14:47:07,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:07,074] [INFO] Task started: Prodigal
[2024-01-24 14:47:07,074] [INFO] Running command: gunzip -c /var/lib/cwl/stg931cd5b7-e5f9-404a-af6b-9bf30f1ad2f6/GCF_019857205.1_ASM1985720v1_genomic.fna.gz | prodigal -d GCF_019857205.1_ASM1985720v1_genomic.fna/cds.fna -a GCF_019857205.1_ASM1985720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:17,540] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:17,540] [INFO] Task started: HMMsearch
[2024-01-24 14:47:17,540] [INFO] Running command: hmmsearch --tblout GCF_019857205.1_ASM1985720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5af8d0a2-e111-4d8e-bbf5-995f72537cc1/dqc_reference/reference_markers.hmm GCF_019857205.1_ASM1985720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:17,825] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:17,825] [INFO] Found 6/6 markers.
[2024-01-24 14:47:17,856] [INFO] Query marker FASTA was written to GCF_019857205.1_ASM1985720v1_genomic.fna/markers.fasta
[2024-01-24 14:47:17,857] [INFO] Task started: Blastn
[2024-01-24 14:47:17,857] [INFO] Running command: blastn -query GCF_019857205.1_ASM1985720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af8d0a2-e111-4d8e-bbf5-995f72537cc1/dqc_reference/reference_markers.fasta -out GCF_019857205.1_ASM1985720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:18,790] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:18,793] [INFO] Selected 10 target genomes.
[2024-01-24 14:47:18,794] [INFO] Target genome list was writen to GCF_019857205.1_ASM1985720v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:18,799] [INFO] Task started: fastANI
[2024-01-24 14:47:18,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg931cd5b7-e5f9-404a-af6b-9bf30f1ad2f6/GCF_019857205.1_ASM1985720v1_genomic.fna.gz --refList GCF_019857205.1_ASM1985720v1_genomic.fna/target_genomes.txt --output GCF_019857205.1_ASM1985720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:26,202] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:26,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5af8d0a2-e111-4d8e-bbf5-995f72537cc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:26,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5af8d0a2-e111-4d8e-bbf5-995f72537cc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:26,214] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:26,214] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:47:26,214] [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 pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	100.0	1140	1142	95	inconclusive
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	96.9156	915	1142	95	inconclusive
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	81.4888	644	1142	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	80.6362	569	1142	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.4514	517	1142	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.9512	462	1142	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	79.9217	426	1142	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.7624	457	1142	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.6838	462	1142	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	79.3088	439	1142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:26,216] [INFO] DFAST Taxonomy check result was written to GCF_019857205.1_ASM1985720v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:26,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:26,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:26,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5af8d0a2-e111-4d8e-bbf5-995f72537cc1/dqc_reference/checkm_data
[2024-01-24 14:47:26,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:26,255] [INFO] Task started: CheckM
[2024-01-24 14:47:26,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019857205.1_ASM1985720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019857205.1_ASM1985720v1_genomic.fna/checkm_input GCF_019857205.1_ASM1985720v1_genomic.fna/checkm_result
[2024-01-24 14:48:01,431] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:01,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:01,450] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:01,450] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:01,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019857205.1_ASM1985720v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:01,451] [INFO] Task started: Blastn
[2024-01-24 14:48:01,452] [INFO] Running command: blastn -query GCF_019857205.1_ASM1985720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af8d0a2-e111-4d8e-bbf5-995f72537cc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_019857205.1_ASM1985720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:03,213] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:03,218] [INFO] Selected 14 target genomes.
[2024-01-24 14:48:03,219] [INFO] Target genome list was writen to GCF_019857205.1_ASM1985720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:03,230] [INFO] Task started: fastANI
[2024-01-24 14:48:03,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg931cd5b7-e5f9-404a-af6b-9bf30f1ad2f6/GCF_019857205.1_ASM1985720v1_genomic.fna.gz --refList GCF_019857205.1_ASM1985720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019857205.1_ASM1985720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:12,091] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:12,104] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:12,104] [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_015767595.1	s__Qipengyuania sp002895025	97.1653	1021	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	conclusive
GCF_001542855.1	s__Qipengyuania sp001542855	81.6614	625	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCA_016764075.1	s__Qipengyuania sp016764075	81.5148	451	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828015.1	s__Qipengyuania citrea	81.2723	581	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_011762005.1	s__Qipengyuania flava	80.6466	568	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_003355455.1	s__Qipengyuania aurea	80.5451	549	1142	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	79.9626	461	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.8095	399	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	79.7517	458	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	79.6838	462	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795865.1	s__Qipengyuania seohaensis	79.3079	439	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911865.1	s__Qipengyuania sp013911865	79.2849	353	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793865.1	s__Qipengyuania sp016793865	78.1131	303	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308255.1	s__Croceibacterium sp001897135	77.9415	262	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:12,106] [INFO] GTDB search result was written to GCF_019857205.1_ASM1985720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:12,107] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:12,111] [INFO] DFAST_QC result json was written to GCF_019857205.1_ASM1985720v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:12,111] [INFO] DFAST_QC completed!
[2024-01-24 14:48:12,111] [INFO] Total running time: 0h1m6s