[2023-06-19 07:17:04,337] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:17:04,340] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:17:04,340] [INFO] DQC Reference Directory: /var/lib/cwl/stg675bcae0-cdd0-4551-bc96-68863fb3855c/dqc_reference
[2023-06-19 07:17:06,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:17:06,559] [INFO] Task started: Prodigal
[2023-06-19 07:17:06,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b1db7ef-b6ab-44ed-98e2-003bcf3895ac/GCA_018828205.1_ASM1882820v1_genomic.fna.gz | prodigal -d GCA_018828205.1_ASM1882820v1_genomic.fna/cds.fna -a GCA_018828205.1_ASM1882820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:17:13,269] [INFO] Task succeeded: Prodigal
[2023-06-19 07:17:13,269] [INFO] Task started: HMMsearch
[2023-06-19 07:17:13,270] [INFO] Running command: hmmsearch --tblout GCA_018828205.1_ASM1882820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg675bcae0-cdd0-4551-bc96-68863fb3855c/dqc_reference/reference_markers.hmm GCA_018828205.1_ASM1882820v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:17:13,510] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:17:13,511] [INFO] Found 6/6 markers.
[2023-06-19 07:17:13,540] [INFO] Query marker FASTA was written to GCA_018828205.1_ASM1882820v1_genomic.fna/markers.fasta
[2023-06-19 07:17:13,541] [INFO] Task started: Blastn
[2023-06-19 07:17:13,541] [INFO] Running command: blastn -query GCA_018828205.1_ASM1882820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg675bcae0-cdd0-4551-bc96-68863fb3855c/dqc_reference/reference_markers.fasta -out GCA_018828205.1_ASM1882820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:17:14,447] [INFO] Task succeeded: Blastn
[2023-06-19 07:17:14,452] [INFO] Selected 25 target genomes.
[2023-06-19 07:17:14,452] [INFO] Target genome list was writen to GCA_018828205.1_ASM1882820v1_genomic.fna/target_genomes.txt
[2023-06-19 07:17:14,462] [INFO] Task started: fastANI
[2023-06-19 07:17:14,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b1db7ef-b6ab-44ed-98e2-003bcf3895ac/GCA_018828205.1_ASM1882820v1_genomic.fna.gz --refList GCA_018828205.1_ASM1882820v1_genomic.fna/target_genomes.txt --output GCA_018828205.1_ASM1882820v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:17:29,714] [INFO] Task succeeded: fastANI
[2023-06-19 07:17:29,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg675bcae0-cdd0-4551-bc96-68863fb3855c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:17:29,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg675bcae0-cdd0-4551-bc96-68863fb3855c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:17:29,738] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:17:29,738] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 07:17:29,739] [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 pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	80.8734	447	737	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.1267	430	737	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	80.0975	393	737	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	80.0178	389	737	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	79.9573	414	737	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.8621	387	737	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.8408	371	737	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.8163	405	737	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.7517	380	737	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.6935	373	737	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	79.5596	321	737	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.5496	336	737	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	79.5249	403	737	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	79.4271	387	737	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	79.4179	390	737	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	79.4064	385	737	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	79.3362	338	737	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.2685	356	737	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	79.1703	321	737	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	79.1649	323	737	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.1126	365	737	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	79.0069	306	737	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.9678	315	737	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	78.5668	279	737	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	78.3744	299	737	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 07:17:29,741] [INFO] DFAST Taxonomy check result was written to GCA_018828205.1_ASM1882820v1_genomic.fna/tc_result.tsv
[2023-06-19 07:17:29,741] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:17:29,742] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:17:29,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg675bcae0-cdd0-4551-bc96-68863fb3855c/dqc_reference/checkm_data
[2023-06-19 07:17:29,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:17:29,776] [INFO] Task started: CheckM
[2023-06-19 07:17:29,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018828205.1_ASM1882820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018828205.1_ASM1882820v1_genomic.fna/checkm_input GCA_018828205.1_ASM1882820v1_genomic.fna/checkm_result
[2023-06-19 07:17:54,326] [INFO] Task succeeded: CheckM
[2023-06-19 07:17:54,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 07:17:54,354] [INFO] ===== Completeness check finished =====
[2023-06-19 07:17:54,354] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:17:54,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018828205.1_ASM1882820v1_genomic.fna/markers.fasta)
[2023-06-19 07:17:54,355] [INFO] Task started: Blastn
[2023-06-19 07:17:54,355] [INFO] Running command: blastn -query GCA_018828205.1_ASM1882820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg675bcae0-cdd0-4551-bc96-68863fb3855c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018828205.1_ASM1882820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:17:55,970] [INFO] Task succeeded: Blastn
[2023-06-19 07:17:55,975] [INFO] Selected 19 target genomes.
[2023-06-19 07:17:55,976] [INFO] Target genome list was writen to GCA_018828205.1_ASM1882820v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:17:56,069] [INFO] Task started: fastANI
[2023-06-19 07:17:56,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b1db7ef-b6ab-44ed-98e2-003bcf3895ac/GCA_018828205.1_ASM1882820v1_genomic.fna.gz --refList GCA_018828205.1_ASM1882820v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018828205.1_ASM1882820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:18:06,887] [INFO] Task succeeded: fastANI
[2023-06-19 07:18:06,907] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 07:18:06,908] [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_018828205.1	s__Qipengyuania sp018828205	100.0	725	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001678665.1	s__Qipengyuania sp001678665	88.0714	565	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	86.6286	399	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_009827295.1	s__Qipengyuania pelagi	80.8685	447	737	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	80.5272	431	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCA_009993605.1	s__Qipengyuania sp009993605	80.4783	442	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	80.2984	429	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_001542855.1	s__Qipengyuania sp001542855	80.1491	413	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_011762005.1	s__Qipengyuania flava	79.9312	416	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.8496	402	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	79.8306	387	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.8266	372	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	79.7915	379	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557325.1	s__Erythrobacter donghaensis_B	79.7813	363	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.70	99.64	0.86	0.85	7	-
GCF_000331285.1	s__Erythrobacter sp000331285	79.6891	349	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	79.6053	351	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	79.5496	336	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822695.1	s__Erythrobacter sp013822695	79.3198	347	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCF_001028625.1	s__Pelagerythrobacter marensis	79.1558	322	737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-19 07:18:06,910] [INFO] GTDB search result was written to GCA_018828205.1_ASM1882820v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:18:06,910] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:18:06,915] [INFO] DFAST_QC result json was written to GCA_018828205.1_ASM1882820v1_genomic.fna/dqc_result.json
[2023-06-19 07:18:06,915] [INFO] DFAST_QC completed!
[2023-06-19 07:18:06,915] [INFO] Total running time: 0h1m3s