[2024-01-24 12:06:33,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg91fd8129-5c1f-4592-a1ba-855ee8923dfa/dqc_reference
[2024-01-24 12:06:34,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,860] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a4527aa-9df4-4c2f-9694-630ce462a3d9/GCF_014641655.1_ASM1464165v1_genomic.fna.gz | prodigal -d GCF_014641655.1_ASM1464165v1_genomic.fna/cds.fna -a GCF_014641655.1_ASM1464165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:42,559] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:42,560] [INFO] Task started: HMMsearch
[2024-01-24 12:06:42,560] [INFO] Running command: hmmsearch --tblout GCF_014641655.1_ASM1464165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91fd8129-5c1f-4592-a1ba-855ee8923dfa/dqc_reference/reference_markers.hmm GCF_014641655.1_ASM1464165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:42,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:42,794] [INFO] Found 6/6 markers.
[2024-01-24 12:06:42,822] [INFO] Query marker FASTA was written to GCF_014641655.1_ASM1464165v1_genomic.fna/markers.fasta
[2024-01-24 12:06:42,823] [INFO] Task started: Blastn
[2024-01-24 12:06:42,823] [INFO] Running command: blastn -query GCF_014641655.1_ASM1464165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91fd8129-5c1f-4592-a1ba-855ee8923dfa/dqc_reference/reference_markers.fasta -out GCF_014641655.1_ASM1464165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:43,856] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:43,860] [INFO] Selected 27 target genomes.
[2024-01-24 12:06:43,861] [INFO] Target genome list was writen to GCF_014641655.1_ASM1464165v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:43,872] [INFO] Task started: fastANI
[2024-01-24 12:06:43,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a4527aa-9df4-4c2f-9694-630ce462a3d9/GCF_014641655.1_ASM1464165v1_genomic.fna.gz --refList GCF_014641655.1_ASM1464165v1_genomic.fna/target_genomes.txt --output GCF_014641655.1_ASM1464165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:00,322] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:00,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91fd8129-5c1f-4592-a1ba-855ee8923dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:00,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91fd8129-5c1f-4592-a1ba-855ee8923dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:00,349] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:00,349] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:00,349] [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 proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.0214	470	861	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.9742	458	861	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.9389	434	861	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.9072	452	861	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.8475	418	861	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.639	431	861	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.6379	415	861	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.6264	432	861	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.5692	418	861	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.5431	426	861	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	79.5373	352	861	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	79.4917	426	861	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.4628	437	861	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.3307	400	861	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	79.2949	407	861	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	79.2525	393	861	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.1943	394	861	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	79.1755	363	861	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.1098	372	861	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	79.1083	435	861	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.9308	317	861	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	78.9124	315	861	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.7184	340	861	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	78.6755	350	861	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.4571	364	861	95	below_threshold
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	78.3694	289	861	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000375445.1	378548	378548	type	True	77.8671	234	861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:00,351] [INFO] DFAST Taxonomy check result was written to GCF_014641655.1_ASM1464165v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:00,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:00,352] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:00,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91fd8129-5c1f-4592-a1ba-855ee8923dfa/dqc_reference/checkm_data
[2024-01-24 12:07:00,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:00,412] [INFO] Task started: CheckM
[2024-01-24 12:07:00,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641655.1_ASM1464165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641655.1_ASM1464165v1_genomic.fna/checkm_input GCF_014641655.1_ASM1464165v1_genomic.fna/checkm_result
[2024-01-24 12:07:27,279] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:27,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:27,303] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:27,303] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:27,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641655.1_ASM1464165v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:27,304] [INFO] Task started: Blastn
[2024-01-24 12:07:27,304] [INFO] Running command: blastn -query GCF_014641655.1_ASM1464165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91fd8129-5c1f-4592-a1ba-855ee8923dfa/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641655.1_ASM1464165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:29,085] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:29,089] [INFO] Selected 23 target genomes.
[2024-01-24 12:07:29,090] [INFO] Target genome list was writen to GCF_014641655.1_ASM1464165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:29,106] [INFO] Task started: fastANI
[2024-01-24 12:07:29,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a4527aa-9df4-4c2f-9694-630ce462a3d9/GCF_014641655.1_ASM1464165v1_genomic.fna.gz --refList GCF_014641655.1_ASM1464165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641655.1_ASM1464165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:43,061] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:43,086] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:43,087] [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_014641655.1	s__Alteriqipengyuania_A marina	100.0	861	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	98.02	98.02	0.89	0.89	2	conclusive
GCF_009827575.1	s__Alteriqipengyuania_A halimionae	82.866	655	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	80.3808	463	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	80.0986	451	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.9755	431	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828205.1	s__Qipengyuania sp018828205	79.7549	373	861	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	79.6682	428	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	79.5683	431	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.543	426	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795865.1	s__Qipengyuania seohaensis	79.5373	352	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993605.1	s__Qipengyuania sp009993605	79.4936	432	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	79.449	390	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	79.3257	401	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331285.1	s__Erythrobacter sp000331285	79.3125	403	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557115.1	s__Erythrobacter sp001557115	79.2979	387	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCF_011320115.1	s__Croceibacterium segetis	79.2224	352	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.9727	330	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408095.1	s__Novosphingobium marinum	78.8841	317	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013370205.1	s__Actirhodobacter atriluteus	78.8267	328	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	78.8064	289	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_014230315.1	s__Novosphingobium flavum	78.7427	338	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874585.1	s__Novosphingobium sp006874585	78.641	330	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_007991615.1	s__Novosphingobium sediminis	78.3699	291	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:43,088] [INFO] GTDB search result was written to GCF_014641655.1_ASM1464165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:43,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:43,095] [INFO] DFAST_QC result json was written to GCF_014641655.1_ASM1464165v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:43,095] [INFO] DFAST_QC completed!
[2024-01-24 12:07:43,095] [INFO] Total running time: 0h1m10s