[2023-03-18 09:46:51,442] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:46:51,442] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:46:51,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg4944d6f3-88dc-4b18-9cb2-29b3b4f1f6d1/dqc_reference
[2023-03-18 09:46:52,574] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:46:52,575] [INFO] Task started: Prodigal
[2023-03-18 09:46:52,575] [INFO] Running command: cat /var/lib/cwl/stg9257231a-8acf-4f04-a2ff-7d5845a6f28c/OceanDNA-b31569.fa | prodigal -d OceanDNA-b31569/cds.fna -a OceanDNA-b31569/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:47:16,173] [INFO] Task succeeded: Prodigal
[2023-03-18 09:47:16,173] [INFO] Task started: HMMsearch
[2023-03-18 09:47:16,173] [INFO] Running command: hmmsearch --tblout OceanDNA-b31569/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4944d6f3-88dc-4b18-9cb2-29b3b4f1f6d1/dqc_reference/reference_markers.hmm OceanDNA-b31569/protein.faa > /dev/null
[2023-03-18 09:47:16,394] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:47:16,395] [INFO] Found 6/6 markers.
[2023-03-18 09:47:16,418] [INFO] Query marker FASTA was written to OceanDNA-b31569/markers.fasta
[2023-03-18 09:47:16,420] [INFO] Task started: Blastn
[2023-03-18 09:47:16,420] [INFO] Running command: blastn -query OceanDNA-b31569/markers.fasta -db /var/lib/cwl/stg4944d6f3-88dc-4b18-9cb2-29b3b4f1f6d1/dqc_reference/reference_markers.fasta -out OceanDNA-b31569/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:47:17,538] [INFO] Task succeeded: Blastn
[2023-03-18 09:47:17,539] [INFO] Selected 24 target genomes.
[2023-03-18 09:47:17,539] [INFO] Target genome list was writen to OceanDNA-b31569/target_genomes.txt
[2023-03-18 09:47:17,554] [INFO] Task started: fastANI
[2023-03-18 09:47:17,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg9257231a-8acf-4f04-a2ff-7d5845a6f28c/OceanDNA-b31569.fa --refList OceanDNA-b31569/target_genomes.txt --output OceanDNA-b31569/fastani_result.tsv --threads 1
[2023-03-18 09:47:37,217] [INFO] Task succeeded: fastANI
[2023-03-18 09:47:37,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4944d6f3-88dc-4b18-9cb2-29b3b4f1f6d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:47:37,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4944d6f3-88dc-4b18-9cb2-29b3b4f1f6d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:47:37,281] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:47:37,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:47:37,281] [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
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	84.8186	903	1251	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	83.3298	817	1251	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.8784	411	1251	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	78.7667	431	1251	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	78.5714	413	1251	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.5174	425	1251	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.4823	411	1251	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.3173	338	1251	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.2217	359	1251	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	78.2079	421	1251	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	78.1609	339	1251	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	78.159	345	1251	95	below_threshold
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	78.0928	345	1251	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	77.9588	316	1251	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	77.9372	313	1251	95	below_threshold
Sphingomonas mucosissima	strain=DSM 17494	GCA_002197665.1	370959	370959	type	True	77.9152	255	1251	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.829	297	1251	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.8255	301	1251	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.8205	358	1251	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	77.7529	306	1251	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.706	295	1251	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	77.6803	217	1251	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.6673	252	1251	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	77.5126	263	1251	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:47:37,282] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31569/tc_result.tsv
[2023-03-18 09:47:37,282] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:47:37,282] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:47:37,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4944d6f3-88dc-4b18-9cb2-29b3b4f1f6d1/dqc_reference/checkm_data
[2023-03-18 09:47:37,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:47:37,623] [INFO] Task started: CheckM
[2023-03-18 09:47:37,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31569/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31569/checkm_input OceanDNA-b31569/checkm_result
[2023-03-18 09:48:38,377] [INFO] Task succeeded: CheckM
[2023-03-18 09:48:38,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:48:38,380] [INFO] ===== Completeness check finished =====
[2023-03-18 09:48:38,380] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:48:38,380] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31569/markers.fasta)
[2023-03-18 09:48:38,381] [INFO] Task started: Blastn
[2023-03-18 09:48:38,381] [INFO] Running command: blastn -query OceanDNA-b31569/markers.fasta -db /var/lib/cwl/stg4944d6f3-88dc-4b18-9cb2-29b3b4f1f6d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31569/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:48:40,339] [INFO] Task succeeded: Blastn
[2023-03-18 09:48:40,340] [INFO] Selected 6 target genomes.
[2023-03-18 09:48:40,340] [INFO] Target genome list was writen to OceanDNA-b31569/target_genomes_gtdb.txt
[2023-03-18 09:48:40,346] [INFO] Task started: fastANI
[2023-03-18 09:48:40,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg9257231a-8acf-4f04-a2ff-7d5845a6f28c/OceanDNA-b31569.fa --refList OceanDNA-b31569/target_genomes_gtdb.txt --output OceanDNA-b31569/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:48:46,342] [INFO] Task succeeded: fastANI
[2023-03-18 09:48:46,346] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:48:46,347] [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_001555775.1	s__Blastomonas delafieldii_A	99.7737	1048	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	99.74	98.25	0.90	0.81	22	conclusive
GCF_013607875.1	s__Blastomonas ursincola	93.3823	1060	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	97.82	97.14	0.88	0.79	7	-
GCA_000503195.1	s__Blastomonas sp000503195	90.6275	1004	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	97.00	97.00	0.84	0.84	2	-
GCF_003201955.1	s__Blastomonas natatoria	88.4489	961	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786215.1	s__Blastomonas sp000786215	85.7681	910	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003431825.1	s__Blastomonas fulva	84.812	904	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	98.01	97.97	0.88	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-18 09:48:46,347] [INFO] GTDB search result was written to OceanDNA-b31569/result_gtdb.tsv
[2023-03-18 09:48:46,347] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:48:46,349] [INFO] DFAST_QC result json was written to OceanDNA-b31569/dqc_result.json
[2023-03-18 09:48:46,349] [INFO] DFAST_QC completed!
[2023-03-18 09:48:46,349] [INFO] Total running time: 0h1m55s