[2024-01-24 13:12:55,710] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:55,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:55,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a3f210a-419b-4225-b468-7f1c8116e85f/dqc_reference
[2024-01-24 13:12:57,181] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,182] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,182] [INFO] Running command: gunzip -c /var/lib/cwl/stg36713344-73bd-4bcc-b549-23dc3a344752/GCF_019711415.1_ASM1971141v1_genomic.fna.gz | prodigal -d GCF_019711415.1_ASM1971141v1_genomic.fna/cds.fna -a GCF_019711415.1_ASM1971141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:05,905] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:05,906] [INFO] Task started: HMMsearch
[2024-01-24 13:13:05,906] [INFO] Running command: hmmsearch --tblout GCF_019711415.1_ASM1971141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a3f210a-419b-4225-b468-7f1c8116e85f/dqc_reference/reference_markers.hmm GCF_019711415.1_ASM1971141v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:06,168] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:06,169] [INFO] Found 6/6 markers.
[2024-01-24 13:13:06,198] [INFO] Query marker FASTA was written to GCF_019711415.1_ASM1971141v1_genomic.fna/markers.fasta
[2024-01-24 13:13:06,198] [INFO] Task started: Blastn
[2024-01-24 13:13:06,198] [INFO] Running command: blastn -query GCF_019711415.1_ASM1971141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a3f210a-419b-4225-b468-7f1c8116e85f/dqc_reference/reference_markers.fasta -out GCF_019711415.1_ASM1971141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:07,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:07,176] [INFO] Selected 10 target genomes.
[2024-01-24 13:13:07,176] [INFO] Target genome list was writen to GCF_019711415.1_ASM1971141v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:07,184] [INFO] Task started: fastANI
[2024-01-24 13:13:07,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg36713344-73bd-4bcc-b549-23dc3a344752/GCF_019711415.1_ASM1971141v1_genomic.fna.gz --refList GCF_019711415.1_ASM1971141v1_genomic.fna/target_genomes.txt --output GCF_019711415.1_ASM1971141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:13,797] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:13,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a3f210a-419b-4225-b468-7f1c8116e85f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:13,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a3f210a-419b-4225-b468-7f1c8116e85f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:13,806] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:13,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:13,807] [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 vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	100.0	902	903	95	conclusive
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	83.7057	641	903	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	83.5309	673	903	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	83.5201	681	903	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	83.4285	642	903	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	83.391	660	903	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	83.309	657	903	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	82.1767	604	903	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	79.6291	399	903	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.1597	404	903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:13,808] [INFO] DFAST Taxonomy check result was written to GCF_019711415.1_ASM1971141v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:13,809] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:13,809] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:13,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a3f210a-419b-4225-b468-7f1c8116e85f/dqc_reference/checkm_data
[2024-01-24 13:13:13,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:13,839] [INFO] Task started: CheckM
[2024-01-24 13:13:13,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019711415.1_ASM1971141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019711415.1_ASM1971141v1_genomic.fna/checkm_input GCF_019711415.1_ASM1971141v1_genomic.fna/checkm_result
[2024-01-24 13:13:43,742] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:43,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:43,761] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:43,761] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:43,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019711415.1_ASM1971141v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:43,762] [INFO] Task started: Blastn
[2024-01-24 13:13:43,763] [INFO] Running command: blastn -query GCF_019711415.1_ASM1971141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a3f210a-419b-4225-b468-7f1c8116e85f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019711415.1_ASM1971141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:45,450] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:45,453] [INFO] Selected 13 target genomes.
[2024-01-24 13:13:45,453] [INFO] Target genome list was writen to GCF_019711415.1_ASM1971141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:45,469] [INFO] Task started: fastANI
[2024-01-24 13:13:45,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg36713344-73bd-4bcc-b549-23dc3a344752/GCF_019711415.1_ASM1971141v1_genomic.fna.gz --refList GCF_019711415.1_ASM1971141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019711415.1_ASM1971141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:53,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:53,539] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:13:53,540] [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_000756795.1	s__Qipengyuania vulgaris_A	83.0935	647	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000181515.1	s__Qipengyuania sp000181515	83.0226	624	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	82.9461	505	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	82.1514	606	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827445.1	s__Qipengyuania aquimaris	81.5507	552	903	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	81.2883	569	903	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	81.0995	554	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	81.0119	540	903	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	80.6728	395	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695185.1	s__Qipengyuania sp002695185	80.2342	456	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	96.33	96.22	0.77	0.72	4	-
GCF_004114695.1	s__Parerythrobacter sp004114695	80.1845	484	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767595.1	s__Qipengyuania sp002895025	79.6725	390	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	79.0715	404	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:53,542] [INFO] GTDB search result was written to GCF_019711415.1_ASM1971141v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:53,542] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:53,556] [INFO] DFAST_QC result json was written to GCF_019711415.1_ASM1971141v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:53,557] [INFO] DFAST_QC completed!
[2024-01-24 13:13:53,557] [INFO] Total running time: 0h0m58s