[2023-03-17 00:17:04,558] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,558] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg7078dd41-2f0e-4a4a-840d-cdb84d2e1e84/dqc_reference
[2023-03-17 00:17:05,694] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,695] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,695] [INFO] Running command: cat /var/lib/cwl/stg3dd8c4e8-dfb5-486a-94a5-cd85f7b1aa71/OceanDNA-b32140.fa | prodigal -d OceanDNA-b32140/cds.fna -a OceanDNA-b32140/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:22,204] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:22,205] [INFO] Task started: HMMsearch
[2023-03-17 00:17:22,205] [INFO] Running command: hmmsearch --tblout OceanDNA-b32140/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7078dd41-2f0e-4a4a-840d-cdb84d2e1e84/dqc_reference/reference_markers.hmm OceanDNA-b32140/protein.faa > /dev/null
[2023-03-17 00:17:22,413] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:22,414] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3dd8c4e8-dfb5-486a-94a5-cd85f7b1aa71/OceanDNA-b32140.fa]
[2023-03-17 00:17:22,432] [INFO] Query marker FASTA was written to OceanDNA-b32140/markers.fasta
[2023-03-17 00:17:22,433] [INFO] Task started: Blastn
[2023-03-17 00:17:22,433] [INFO] Running command: blastn -query OceanDNA-b32140/markers.fasta -db /var/lib/cwl/stg7078dd41-2f0e-4a4a-840d-cdb84d2e1e84/dqc_reference/reference_markers.fasta -out OceanDNA-b32140/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:23,247] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:23,248] [INFO] Selected 19 target genomes.
[2023-03-17 00:17:23,248] [INFO] Target genome list was writen to OceanDNA-b32140/target_genomes.txt
[2023-03-17 00:17:23,258] [INFO] Task started: fastANI
[2023-03-17 00:17:23,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd8c4e8-dfb5-486a-94a5-cd85f7b1aa71/OceanDNA-b32140.fa --refList OceanDNA-b32140/target_genomes.txt --output OceanDNA-b32140/fastani_result.tsv --threads 1
[2023-03-17 00:17:37,219] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:37,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7078dd41-2f0e-4a4a-840d-cdb84d2e1e84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:37,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7078dd41-2f0e-4a4a-840d-cdb84d2e1e84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:37,230] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:37,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:17:37,230] [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
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	84.7448	653	891	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	82.5199	555	891	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	82.4982	558	891	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	82.4359	557	891	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	81.5716	504	891	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	79.7244	446	891	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.659	449	891	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.6299	443	891	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	79.2162	386	891	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.1903	403	891	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.1795	362	891	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	79.1722	356	891	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	79.124	418	891	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	79.0388	407	891	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	78.8814	370	891	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.877	368	891	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	78.8667	322	891	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.8076	366	891	95	below_threshold
Sphingomonas xinjiangensis	strain=DSM 26736	GCA_014199255.1	643568	643568	type	True	78.5958	315	891	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:17:37,230] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32140/tc_result.tsv
[2023-03-17 00:17:37,231] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:37,231] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:37,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7078dd41-2f0e-4a4a-840d-cdb84d2e1e84/dqc_reference/checkm_data
[2023-03-17 00:17:37,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:37,236] [INFO] Task started: CheckM
[2023-03-17 00:17:37,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32140/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32140/checkm_input OceanDNA-b32140/checkm_result
[2023-03-17 00:18:20,142] [INFO] Task succeeded: CheckM
[2023-03-17 00:18:20,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:18:20,185] [INFO] ===== Completeness check finished =====
[2023-03-17 00:18:20,186] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:18:20,186] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32140/markers.fasta)
[2023-03-17 00:18:20,187] [INFO] Task started: Blastn
[2023-03-17 00:18:20,187] [INFO] Running command: blastn -query OceanDNA-b32140/markers.fasta -db /var/lib/cwl/stg7078dd41-2f0e-4a4a-840d-cdb84d2e1e84/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32140/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:18:21,621] [INFO] Task succeeded: Blastn
[2023-03-17 00:18:21,622] [INFO] Selected 15 target genomes.
[2023-03-17 00:18:21,622] [INFO] Target genome list was writen to OceanDNA-b32140/target_genomes_gtdb.txt
[2023-03-17 00:18:21,657] [INFO] Task started: fastANI
[2023-03-17 00:18:21,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd8c4e8-dfb5-486a-94a5-cd85f7b1aa71/OceanDNA-b32140.fa --refList OceanDNA-b32140/target_genomes_gtdb.txt --output OceanDNA-b32140/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:18:32,158] [INFO] Task succeeded: fastANI
[2023-03-17 00:18:32,169] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:18:32,169] [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_002280565.1	s__Sphingomonas sp002280565	96.8646	551	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.98	96.98	0.90	0.90	2	conclusive
GCF_001557215.1	s__Sphingomonas sp001557215	89.335	618	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_007833215.1	s__Sphingomonas sp007833215	84.7292	654	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797435.1	s__Sphingomonas koreensis	82.5199	555	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCA_902826325.1	s__Sphingomonas sp902826325	82.2791	405	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCF_001721295.1	s__Sphingomonas turrisvirgatae	81.5517	506	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	79.6343	443	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012927115.1	s__Sphingomonas sp012927115	79.5343	432	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	79.3865	365	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_001421355.1	s__Sphingomonas sp001421355	79.2189	365	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
GCF_001591025.1	s__Sphingomonas soli	79.2038	387	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	79.1692	344	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346325.1	s__Sphingomonas japonica	79.1081	355	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017745215.1	s__Sphingomonas sp017745215	79.0825	423	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421765.1	s__Sphingomonas sp001421765	78.9799	381	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-17 00:18:32,169] [INFO] GTDB search result was written to OceanDNA-b32140/result_gtdb.tsv
[2023-03-17 00:18:32,169] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:18:32,171] [INFO] DFAST_QC result json was written to OceanDNA-b32140/dqc_result.json
[2023-03-17 00:18:32,171] [INFO] DFAST_QC completed!
[2023-03-17 00:18:32,171] [INFO] Total running time: 0h1m28s