[2024-01-24 12:44:19,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:19,014] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:19,014] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc17e646-1ba1-44df-8e9d-6d03bea30180/dqc_reference
[2024-01-24 12:44:20,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:20,207] [INFO] Task started: Prodigal
[2024-01-24 12:44:20,207] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5d376ab-741a-4fd3-b7f6-d9018bc3b321/GCF_019711375.1_ASM1971137v1_genomic.fna.gz | prodigal -d GCF_019711375.1_ASM1971137v1_genomic.fna/cds.fna -a GCF_019711375.1_ASM1971137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:28,662] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:28,663] [INFO] Task started: HMMsearch
[2024-01-24 12:44:28,663] [INFO] Running command: hmmsearch --tblout GCF_019711375.1_ASM1971137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc17e646-1ba1-44df-8e9d-6d03bea30180/dqc_reference/reference_markers.hmm GCF_019711375.1_ASM1971137v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:28,885] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:28,887] [INFO] Found 6/6 markers.
[2024-01-24 12:44:28,918] [INFO] Query marker FASTA was written to GCF_019711375.1_ASM1971137v1_genomic.fna/markers.fasta
[2024-01-24 12:44:28,918] [INFO] Task started: Blastn
[2024-01-24 12:44:28,918] [INFO] Running command: blastn -query GCF_019711375.1_ASM1971137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc17e646-1ba1-44df-8e9d-6d03bea30180/dqc_reference/reference_markers.fasta -out GCF_019711375.1_ASM1971137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:29,867] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:29,871] [INFO] Selected 8 target genomes.
[2024-01-24 12:44:29,871] [INFO] Target genome list was writen to GCF_019711375.1_ASM1971137v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:29,933] [INFO] Task started: fastANI
[2024-01-24 12:44:29,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5d376ab-741a-4fd3-b7f6-d9018bc3b321/GCF_019711375.1_ASM1971137v1_genomic.fna.gz --refList GCF_019711375.1_ASM1971137v1_genomic.fna/target_genomes.txt --output GCF_019711375.1_ASM1971137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:35,159] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:35,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc17e646-1ba1-44df-8e9d-6d03bea30180/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:35,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc17e646-1ba1-44df-8e9d-6d03bea30180/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:35,175] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:35,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:35,176] [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 aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	100.0	940	941	95	conclusive
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	85.3352	734	941	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	84.5755	696	941	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	84.1419	692	941	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	84.1351	684	941	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	83.9836	683	941	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	83.2391	660	941	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	81.9186	552	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:35,178] [INFO] DFAST Taxonomy check result was written to GCF_019711375.1_ASM1971137v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:35,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:35,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:35,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc17e646-1ba1-44df-8e9d-6d03bea30180/dqc_reference/checkm_data
[2024-01-24 12:44:35,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:35,209] [INFO] Task started: CheckM
[2024-01-24 12:44:35,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019711375.1_ASM1971137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019711375.1_ASM1971137v1_genomic.fna/checkm_input GCF_019711375.1_ASM1971137v1_genomic.fna/checkm_result
[2024-01-24 12:45:03,986] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:03,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:04,008] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:04,008] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:04,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019711375.1_ASM1971137v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:04,009] [INFO] Task started: Blastn
[2024-01-24 12:45:04,009] [INFO] Running command: blastn -query GCF_019711375.1_ASM1971137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc17e646-1ba1-44df-8e9d-6d03bea30180/dqc_reference/reference_markers_gtdb.fasta -out GCF_019711375.1_ASM1971137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:05,813] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:05,817] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:05,817] [INFO] Target genome list was writen to GCF_019711375.1_ASM1971137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:05,871] [INFO] Task started: fastANI
[2024-01-24 12:45:05,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5d376ab-741a-4fd3-b7f6-d9018bc3b321/GCF_019711375.1_ASM1971137v1_genomic.fna.gz --refList GCF_019711375.1_ASM1971137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019711375.1_ASM1971137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:15,388] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:15,406] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:45:15,406] [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_000181515.1	s__Qipengyuania sp000181515	89.7647	766	941	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	85.1082	714	941	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	83.2207	545	941	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	82.6782	651	941	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	82.3257	619	941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115585.1	s__Qipengyuania nanhaisediminis	82.2541	634	941	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	81.9404	499	941	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	81.7497	603	941	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	81.6768	607	941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	81.5996	455	941	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	81.3654	571	941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCA_002695185.1	s__Qipengyuania sp002695185	80.909	506	941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	96.33	96.22	0.77	0.72	4	-
GCF_009827295.1	s__Qipengyuania pelagi	80.3254	543	941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	79.448	395	941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:15,408] [INFO] GTDB search result was written to GCF_019711375.1_ASM1971137v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:15,409] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:15,412] [INFO] DFAST_QC result json was written to GCF_019711375.1_ASM1971137v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:15,412] [INFO] DFAST_QC completed!
[2024-01-24 12:45:15,412] [INFO] Total running time: 0h0m56s