[2023-03-14 11:14:12,740] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0c14a07-7436-4f33-a392-cbcd8996a2ef/dqc_reference
[2023-03-14 11:14:14,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,203] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,203] [INFO] Running command: cat /var/lib/cwl/stg13ac9716-014c-4baa-8768-bd64b0036c12/OceanDNA-b32173.fa | prodigal -d OceanDNA-b32173/cds.fna -a OceanDNA-b32173/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:21,152] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:21,153] [INFO] Task started: HMMsearch
[2023-03-14 11:14:21,153] [INFO] Running command: hmmsearch --tblout OceanDNA-b32173/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0c14a07-7436-4f33-a392-cbcd8996a2ef/dqc_reference/reference_markers.hmm OceanDNA-b32173/protein.faa > /dev/null
[2023-03-14 11:14:21,356] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:21,356] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg13ac9716-014c-4baa-8768-bd64b0036c12/OceanDNA-b32173.fa]
[2023-03-14 11:14:21,374] [INFO] Query marker FASTA was written to OceanDNA-b32173/markers.fasta
[2023-03-14 11:14:21,374] [INFO] Task started: Blastn
[2023-03-14 11:14:21,374] [INFO] Running command: blastn -query OceanDNA-b32173/markers.fasta -db /var/lib/cwl/stgf0c14a07-7436-4f33-a392-cbcd8996a2ef/dqc_reference/reference_markers.fasta -out OceanDNA-b32173/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:21,989] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:21,990] [INFO] Selected 15 target genomes.
[2023-03-14 11:14:21,991] [INFO] Target genome list was writen to OceanDNA-b32173/target_genomes.txt
[2023-03-14 11:14:22,002] [INFO] Task started: fastANI
[2023-03-14 11:14:22,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg13ac9716-014c-4baa-8768-bd64b0036c12/OceanDNA-b32173.fa --refList OceanDNA-b32173/target_genomes.txt --output OceanDNA-b32173/fastani_result.tsv --threads 1
[2023-03-14 11:14:31,531] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:31,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0c14a07-7436-4f33-a392-cbcd8996a2ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:31,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0c14a07-7436-4f33-a392-cbcd8996a2ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:31,549] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 11:14:31,549] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 11:14:31,550] [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
Novosphingopyxis iocasae	strain=PB63	GCA_014334095.1	2762729	2762729	type	True	96.5079	274	298	95	conclusive
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	80.6586	208	298	95	below_threshold
Sphingorhabdus soli	strain=D-2Q-5-6	GCA_007995095.1	2601267	2601267	type	True	77.1182	63	298	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	76.9428	59	298	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	76.7012	65	298	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	76.6815	62	298	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	76.6376	69	298	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.5596	65	298	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	76.5357	59	298	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	76.5099	64	298	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	76.4238	64	298	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.2321	65	298	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:31,550] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32173/tc_result.tsv
[2023-03-14 11:14:31,551] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:31,551] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:31,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0c14a07-7436-4f33-a392-cbcd8996a2ef/dqc_reference/checkm_data
[2023-03-14 11:14:31,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:31,713] [INFO] Task started: CheckM
[2023-03-14 11:14:31,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32173/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32173/checkm_input OceanDNA-b32173/checkm_result
[2023-03-14 11:14:54,473] [INFO] Task succeeded: CheckM
[2023-03-14 11:14:54,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.52%
Contamintation: 1.04%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 11:14:54,476] [INFO] ===== Completeness check finished =====
[2023-03-14 11:14:54,476] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:14:54,476] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32173/markers.fasta)
[2023-03-14 11:14:54,477] [INFO] Task started: Blastn
[2023-03-14 11:14:54,477] [INFO] Running command: blastn -query OceanDNA-b32173/markers.fasta -db /var/lib/cwl/stgf0c14a07-7436-4f33-a392-cbcd8996a2ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32173/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:55,501] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:55,502] [INFO] Selected 12 target genomes.
[2023-03-14 11:14:55,502] [INFO] Target genome list was writen to OceanDNA-b32173/target_genomes_gtdb.txt
[2023-03-14 11:14:55,518] [INFO] Task started: fastANI
[2023-03-14 11:14:55,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg13ac9716-014c-4baa-8768-bd64b0036c12/OceanDNA-b32173.fa --refList OceanDNA-b32173/target_genomes_gtdb.txt --output OceanDNA-b32173/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:02,799] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:02,806] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:15:02,806] [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_014334095.1	s__Novosphingopyxis sp002683755	96.5079	274	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingopyxis	95.0	96.10	95.99	0.84	0.79	3	conclusive
GCF_000420305.1	s__Novosphingopyxis baekryungensis	80.6586	208	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720115.1	s__Sphingorhabdus_B sp016720115	76.8992	52	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.85	99.81	0.95	0.95	3	-
GCF_002556635.1	s__Novosphingobium sp002556635	76.8162	64	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974765.1	s__Sphingomonas_B changbaiensis	76.7649	55	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	76.6376	69	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598815.1	s__Sphingopyxis terrae	76.5357	59	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.70	95.58	0.84	0.76	19	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	76.4786	61	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873485.1	s__Sphingopyxis sp014873485	76.2676	70	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240865.1	s__Sphingomonas_B sp018240865	76.1767	66	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:02,807] [INFO] GTDB search result was written to OceanDNA-b32173/result_gtdb.tsv
[2023-03-14 11:15:02,807] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:02,808] [INFO] DFAST_QC result json was written to OceanDNA-b32173/dqc_result.json
[2023-03-14 11:15:02,808] [INFO] DFAST_QC completed!
[2023-03-14 11:15:02,808] [INFO] Total running time: 0h0m50s