[2023-03-17 08:11:32,525] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,526] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg62717e3b-664f-41a8-8b73-da538a79ef0d/dqc_reference
[2023-03-17 08:11:33,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:33,678] [INFO] Task started: Prodigal
[2023-03-17 08:11:33,678] [INFO] Running command: cat /var/lib/cwl/stgf3087e19-d397-43d2-86c4-ca2dac0f5c79/OceanDNA-b29546.fa | prodigal -d OceanDNA-b29546/cds.fna -a OceanDNA-b29546/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:50,106] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:50,106] [INFO] Task started: HMMsearch
[2023-03-17 08:11:50,106] [INFO] Running command: hmmsearch --tblout OceanDNA-b29546/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62717e3b-664f-41a8-8b73-da538a79ef0d/dqc_reference/reference_markers.hmm OceanDNA-b29546/protein.faa > /dev/null
[2023-03-17 08:11:50,293] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:50,294] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf3087e19-d397-43d2-86c4-ca2dac0f5c79/OceanDNA-b29546.fa]
[2023-03-17 08:11:50,315] [INFO] Query marker FASTA was written to OceanDNA-b29546/markers.fasta
[2023-03-17 08:11:50,316] [INFO] Task started: Blastn
[2023-03-17 08:11:50,316] [INFO] Running command: blastn -query OceanDNA-b29546/markers.fasta -db /var/lib/cwl/stg62717e3b-664f-41a8-8b73-da538a79ef0d/dqc_reference/reference_markers.fasta -out OceanDNA-b29546/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:51,150] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:51,151] [INFO] Selected 29 target genomes.
[2023-03-17 08:11:51,151] [INFO] Target genome list was writen to OceanDNA-b29546/target_genomes.txt
[2023-03-17 08:11:51,166] [INFO] Task started: fastANI
[2023-03-17 08:11:51,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3087e19-d397-43d2-86c4-ca2dac0f5c79/OceanDNA-b29546.fa --refList OceanDNA-b29546/target_genomes.txt --output OceanDNA-b29546/fastani_result.tsv --threads 1
[2023-03-17 08:12:11,436] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:11,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62717e3b-664f-41a8-8b73-da538a79ef0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:12:11,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62717e3b-664f-41a8-8b73-da538a79ef0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:12:11,452] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:12:11,452] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:12:11,452] [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
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	80.5885	610	937	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	79.1319	448	937	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	79.121	429	937	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	79.0783	400	937	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.9766	412	937	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.8291	413	937	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	78.7399	413	937	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	78.7244	393	937	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	78.7003	355	937	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.677	392	937	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	78.5035	331	937	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.462	421	937	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.3774	379	937	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.3004	403	937	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.288	416	937	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.2859	387	937	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2529	391	937	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.2519	421	937	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.2255	395	937	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.192	399	937	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.1755	397	937	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	78.039	366	937	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	77.8934	358	937	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	77.8902	324	937	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.8714	325	937	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.7071	334	937	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.623	309	937	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	77.4871	280	937	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	77.2949	273	937	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:12:11,453] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29546/tc_result.tsv
[2023-03-17 08:12:11,453] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:12:11,453] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:12:11,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62717e3b-664f-41a8-8b73-da538a79ef0d/dqc_reference/checkm_data
[2023-03-17 08:12:11,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:12:11,528] [INFO] Task started: CheckM
[2023-03-17 08:12:11,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29546/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29546/checkm_input OceanDNA-b29546/checkm_result
[2023-03-17 08:12:54,029] [INFO] Task succeeded: CheckM
[2023-03-17 08:12:54,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:12:54,032] [INFO] ===== Completeness check finished =====
[2023-03-17 08:12:54,032] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:12:54,032] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29546/markers.fasta)
[2023-03-17 08:12:54,033] [INFO] Task started: Blastn
[2023-03-17 08:12:54,033] [INFO] Running command: blastn -query OceanDNA-b29546/markers.fasta -db /var/lib/cwl/stg62717e3b-664f-41a8-8b73-da538a79ef0d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29546/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:12:55,534] [INFO] Task succeeded: Blastn
[2023-03-17 08:12:55,535] [INFO] Selected 14 target genomes.
[2023-03-17 08:12:55,535] [INFO] Target genome list was writen to OceanDNA-b29546/target_genomes_gtdb.txt
[2023-03-17 08:12:55,658] [INFO] Task started: fastANI
[2023-03-17 08:12:55,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3087e19-d397-43d2-86c4-ca2dac0f5c79/OceanDNA-b29546.fa --refList OceanDNA-b29546/target_genomes_gtdb.txt --output OceanDNA-b29546/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:13:06,089] [INFO] Task succeeded: fastANI
[2023-03-17 08:13:06,098] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:13:06,098] [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_011620265.1	s__Albidovulum sp011620265	89.598	756	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280515.1	s__Albidovulum sp002280515	89.0953	773	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933605.1	s__Albidovulum sp008933605	82.472	580	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841115.1	s__Albidovulum sp002841115	81.4112	574	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973535.1	s__Albidovulum denitrificans	81.0519	611	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302475.1	s__Albidovulum aquaemixtae	80.5969	610	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440625.1	s__Albidovulum sp002440625	80.3684	478	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240425.1	s__TMP-24 sp018240425	79.9559	478	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCF_004010155.1	s__Solirhodobacter olei	79.1458	432	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440945.1	s__QY30 sp002440945	78.6429	227	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QY30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	78.4222	429	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.31	402	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172265.1	s__Roseivivax jejudonensis	77.8934	358	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	77.2855	274	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-17 08:13:06,099] [INFO] GTDB search result was written to OceanDNA-b29546/result_gtdb.tsv
[2023-03-17 08:13:06,099] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:13:06,102] [INFO] DFAST_QC result json was written to OceanDNA-b29546/dqc_result.json
[2023-03-17 08:13:06,102] [INFO] DFAST_QC completed!
[2023-03-17 08:13:06,102] [INFO] Total running time: 0h1m34s