[2024-01-24 13:17:11,483] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:11,485] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:11,485] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2197901-18ce-4684-91c8-45b832f519b2/dqc_reference
[2024-01-24 13:17:12,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:12,697] [INFO] Task started: Prodigal
[2024-01-24 13:17:12,697] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1d25b7a-ded4-46f3-9ccc-3fae57e30b16/GCF_019711355.1_ASM1971135v1_genomic.fna.gz | prodigal -d GCF_019711355.1_ASM1971135v1_genomic.fna/cds.fna -a GCF_019711355.1_ASM1971135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:21,230] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:21,231] [INFO] Task started: HMMsearch
[2024-01-24 13:17:21,231] [INFO] Running command: hmmsearch --tblout GCF_019711355.1_ASM1971135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2197901-18ce-4684-91c8-45b832f519b2/dqc_reference/reference_markers.hmm GCF_019711355.1_ASM1971135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:21,466] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:21,468] [INFO] Found 6/6 markers.
[2024-01-24 13:17:21,498] [INFO] Query marker FASTA was written to GCF_019711355.1_ASM1971135v1_genomic.fna/markers.fasta
[2024-01-24 13:17:21,499] [INFO] Task started: Blastn
[2024-01-24 13:17:21,499] [INFO] Running command: blastn -query GCF_019711355.1_ASM1971135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2197901-18ce-4684-91c8-45b832f519b2/dqc_reference/reference_markers.fasta -out GCF_019711355.1_ASM1971135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:22,323] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:22,327] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:22,328] [INFO] Target genome list was writen to GCF_019711355.1_ASM1971135v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:22,534] [INFO] Task started: fastANI
[2024-01-24 13:17:22,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d25b7a-ded4-46f3-9ccc-3fae57e30b16/GCF_019711355.1_ASM1971135v1_genomic.fna.gz --refList GCF_019711355.1_ASM1971135v1_genomic.fna/target_genomes.txt --output GCF_019711355.1_ASM1971135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:31,382] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:31,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2197901-18ce-4684-91c8-45b832f519b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:31,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2197901-18ce-4684-91c8-45b832f519b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:31,399] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:31,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:31,399] [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 psychrotolerans	strain=1XM2-8	GCA_019711355.1	2867238	2867238	type	True	100.0	914	914	95	conclusive
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	81.482	580	914	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	81.0696	590	914	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	81.0146	579	914	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	80.9264	605	914	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.883	614	914	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	80.2452	533	914	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	80.226	540	914	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	80.2231	534	914	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.9863	488	914	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.9183	517	914	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.7892	493	914	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	79.5783	399	914	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	79.5562	430	914	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.5074	479	914	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.6674	369	914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:31,401] [INFO] DFAST Taxonomy check result was written to GCF_019711355.1_ASM1971135v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:31,401] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:31,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:31,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2197901-18ce-4684-91c8-45b832f519b2/dqc_reference/checkm_data
[2024-01-24 13:17:31,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:31,434] [INFO] Task started: CheckM
[2024-01-24 13:17:31,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019711355.1_ASM1971135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019711355.1_ASM1971135v1_genomic.fna/checkm_input GCF_019711355.1_ASM1971135v1_genomic.fna/checkm_result
[2024-01-24 13:18:00,732] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:00,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:00,757] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:00,758] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:00,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019711355.1_ASM1971135v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:00,759] [INFO] Task started: Blastn
[2024-01-24 13:18:00,759] [INFO] Running command: blastn -query GCF_019711355.1_ASM1971135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2197901-18ce-4684-91c8-45b832f519b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_019711355.1_ASM1971135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:02,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:02,254] [INFO] Selected 16 target genomes.
[2024-01-24 13:18:02,255] [INFO] Target genome list was writen to GCF_019711355.1_ASM1971135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:02,317] [INFO] Task started: fastANI
[2024-01-24 13:18:02,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d25b7a-ded4-46f3-9ccc-3fae57e30b16/GCF_019711355.1_ASM1971135v1_genomic.fna.gz --refList GCF_019711355.1_ASM1971135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019711355.1_ASM1971135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:11,117] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:11,138] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:18:11,138] [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_900115585.1	s__Qipengyuania nanhaisediminis	81.4736	581	914	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	81.0146	579	914	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	80.9264	605	914	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	80.8724	615	914	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	80.0569	494	914	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	79.8733	491	914	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	79.8682	426	914	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	79.7819	422	914	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	79.4335	353	914	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	79.3866	434	914	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	79.2747	345	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355455.1	s__Qipengyuania aurea	79.1942	423	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.0193	367	914	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	78.7801	369	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_900177715.1	s__Erythrobacter xiamenensis	78.6458	344	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677335.1	s__Erythrobacter dokdonensis	77.9705	285	914	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:11,140] [INFO] GTDB search result was written to GCF_019711355.1_ASM1971135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:11,141] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:11,146] [INFO] DFAST_QC result json was written to GCF_019711355.1_ASM1971135v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:11,146] [INFO] DFAST_QC completed!
[2024-01-24 13:18:11,146] [INFO] Total running time: 0h0m60s