[2023-03-15 10:52:57,299] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,299] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e0d07b1-4eb6-4651-8cb3-070bfb6f3c5d/dqc_reference
[2023-03-15 10:52:58,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,863] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,863] [INFO] Running command: cat /var/lib/cwl/stg67b3d07f-5bd9-4864-8d20-244d943c70fb/OceanDNA-b31554.fa | prodigal -d OceanDNA-b31554/cds.fna -a OceanDNA-b31554/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:15,380] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:15,380] [INFO] Task started: HMMsearch
[2023-03-15 10:53:15,380] [INFO] Running command: hmmsearch --tblout OceanDNA-b31554/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e0d07b1-4eb6-4651-8cb3-070bfb6f3c5d/dqc_reference/reference_markers.hmm OceanDNA-b31554/protein.faa > /dev/null
[2023-03-15 10:53:15,558] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:15,558] [INFO] Found 6/6 markers.
[2023-03-15 10:53:15,575] [INFO] Query marker FASTA was written to OceanDNA-b31554/markers.fasta
[2023-03-15 10:53:15,576] [INFO] Task started: Blastn
[2023-03-15 10:53:15,576] [INFO] Running command: blastn -query OceanDNA-b31554/markers.fasta -db /var/lib/cwl/stg2e0d07b1-4eb6-4651-8cb3-070bfb6f3c5d/dqc_reference/reference_markers.fasta -out OceanDNA-b31554/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:16,293] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:16,294] [INFO] Selected 24 target genomes.
[2023-03-15 10:53:16,294] [INFO] Target genome list was writen to OceanDNA-b31554/target_genomes.txt
[2023-03-15 10:53:16,312] [INFO] Task started: fastANI
[2023-03-15 10:53:16,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b3d07f-5bd9-4864-8d20-244d943c70fb/OceanDNA-b31554.fa --refList OceanDNA-b31554/target_genomes.txt --output OceanDNA-b31554/fastani_result.tsv --threads 1
[2023-03-15 10:53:31,144] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:31,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e0d07b1-4eb6-4651-8cb3-070bfb6f3c5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:31,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e0d07b1-4eb6-4651-8cb3-070bfb6f3c5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:31,157] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:31,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:53:31,157] [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
Altererythrobacter ishigakiensis	strain=NBRC 107699	GCA_001663155.1	476157	476157	type	True	85.3125	544	851	95	below_threshold
Altererythrobacter ishigakiensis	strain=ATCC BAA-2084	GCA_007830695.1	476157	476157	type	True	85.2301	543	851	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	78.1146	290	851	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.8626	224	851	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.7778	231	851	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.6541	227	851	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	77.6088	204	851	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.4843	237	851	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	77.3783	206	851	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.375	197	851	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	77.3715	203	851	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.3242	202	851	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.2462	168	851	95	below_threshold
Erythrobacter longus	strain=DSM 6997	GCA_000715015.1	1044	1044	type	True	77.2412	171	851	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	77.2248	157	851	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.0369	185	851	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	76.9458	136	851	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.8177	191	851	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	76.6322	105	851	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	76.0758	76	851	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:53:31,157] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31554/tc_result.tsv
[2023-03-15 10:53:31,157] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:31,158] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:31,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e0d07b1-4eb6-4651-8cb3-070bfb6f3c5d/dqc_reference/checkm_data
[2023-03-15 10:53:31,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:31,162] [INFO] Task started: CheckM
[2023-03-15 10:53:31,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31554/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31554/checkm_input OceanDNA-b31554/checkm_result
[2023-03-15 10:54:14,357] [INFO] Task succeeded: CheckM
[2023-03-15 10:54:14,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:54:14,360] [INFO] ===== Completeness check finished =====
[2023-03-15 10:54:14,360] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:54:14,360] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31554/markers.fasta)
[2023-03-15 10:54:14,361] [INFO] Task started: Blastn
[2023-03-15 10:54:14,362] [INFO] Running command: blastn -query OceanDNA-b31554/markers.fasta -db /var/lib/cwl/stg2e0d07b1-4eb6-4651-8cb3-070bfb6f3c5d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31554/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:54:15,645] [INFO] Task succeeded: Blastn
[2023-03-15 10:54:15,645] [INFO] Selected 23 target genomes.
[2023-03-15 10:54:15,646] [INFO] Target genome list was writen to OceanDNA-b31554/target_genomes_gtdb.txt
[2023-03-15 10:54:15,699] [INFO] Task started: fastANI
[2023-03-15 10:54:15,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b3d07f-5bd9-4864-8d20-244d943c70fb/OceanDNA-b31554.fa --refList OceanDNA-b31554/target_genomes_gtdb.txt --output OceanDNA-b31554/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:54:28,538] [INFO] Task succeeded: fastANI
[2023-03-15 10:54:28,551] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:54:28,551] [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_001663155.1	s__Erythrobacter ishigakiensis	85.3125	544	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	97.03	96.25	0.95	0.94	6	-
GCA_013002295.1	s__Erythrobacter sp013002295	81.3972	357	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.14	98.90	0.85	0.82	4	-
GCA_003149575.1	s__Erythrobacter sp003149575	81.0671	430	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	98.16	98.16	0.93	0.93	2	-
GCF_011047315.1	s__Erythrobacter sp011047315	78.7864	421	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001515985.1	s__Erythrobacter sp001515985	78.394	262	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371495.1	s__Erythrobacter sp013371495	78.1146	290	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	78.1025	247	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	78.0687	322	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	77.5355	192	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	77.4011	169	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363635.1	s__Erythrobacter sp009363635	77.3909	242	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226465.1	s__Erythrobacter sp006226465	77.3792	138	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828055.1	s__Erythrobacter ramosus	77.3783	206	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002706445.1	s__Erythrobacter sp002706445	77.2783	168	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905735.1	s__Erythrobacter sp009905735	77.2755	220	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	77.2138	187	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_001296025.1	s__Erythrobacter sp001296025	77.204	229	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214365.1	s__Erythrobacter sp013214365	77.1661	125	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002215495.1	s__Erythrobacter sp002215495	77.1455	202	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744315.1	s__Croceibacterium sp017744315	76.9125	122	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	76.5516	111	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_012035195.1	s__Sphingomonas sp012035195	76.0758	76	851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:54:28,551] [INFO] GTDB search result was written to OceanDNA-b31554/result_gtdb.tsv
[2023-03-15 10:54:28,552] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:54:28,554] [INFO] DFAST_QC result json was written to OceanDNA-b31554/dqc_result.json
[2023-03-15 10:54:28,554] [INFO] DFAST_QC completed!
[2023-03-15 10:54:28,554] [INFO] Total running time: 0h1m31s