[2023-03-16 17:50:13,084] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:50:13,085] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:50:13,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg273f6dee-b35e-48ce-bf8f-7fe10e48cb72/dqc_reference
[2023-03-16 17:50:14,184] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:50:14,184] [INFO] Task started: Prodigal
[2023-03-16 17:50:14,185] [INFO] Running command: cat /var/lib/cwl/stg3f272fcc-aad4-435b-a962-640e8de24f26/OceanDNA-b33243.fa | prodigal -d OceanDNA-b33243/cds.fna -a OceanDNA-b33243/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:50:33,157] [INFO] Task succeeded: Prodigal
[2023-03-16 17:50:33,157] [INFO] Task started: HMMsearch
[2023-03-16 17:50:33,157] [INFO] Running command: hmmsearch --tblout OceanDNA-b33243/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg273f6dee-b35e-48ce-bf8f-7fe10e48cb72/dqc_reference/reference_markers.hmm OceanDNA-b33243/protein.faa > /dev/null
[2023-03-16 17:50:33,536] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:50:33,537] [INFO] Found 6/6 markers.
[2023-03-16 17:50:33,572] [INFO] Query marker FASTA was written to OceanDNA-b33243/markers.fasta
[2023-03-16 17:50:33,573] [INFO] Task started: Blastn
[2023-03-16 17:50:33,573] [INFO] Running command: blastn -query OceanDNA-b33243/markers.fasta -db /var/lib/cwl/stg273f6dee-b35e-48ce-bf8f-7fe10e48cb72/dqc_reference/reference_markers.fasta -out OceanDNA-b33243/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:50:35,421] [INFO] Task succeeded: Blastn
[2023-03-16 17:50:35,423] [INFO] Selected 34 target genomes.
[2023-03-16 17:50:35,423] [INFO] Target genome list was writen to OceanDNA-b33243/target_genomes.txt
[2023-03-16 17:50:35,449] [INFO] Task started: fastANI
[2023-03-16 17:50:35,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f272fcc-aad4-435b-a962-640e8de24f26/OceanDNA-b33243.fa --refList OceanDNA-b33243/target_genomes.txt --output OceanDNA-b33243/fastani_result.tsv --threads 1
[2023-03-16 17:51:01,482] [INFO] Task succeeded: fastANI
[2023-03-16 17:51:01,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg273f6dee-b35e-48ce-bf8f-7fe10e48cb72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:51:01,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg273f6dee-b35e-48ce-bf8f-7fe10e48cb72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:51:01,500] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:51:01,500] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:51:01,501] [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
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.0391	146	914	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.9979	134	914	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.9782	165	914	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.9559	157	914	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	76.928	178	914	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	76.9175	158	914	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	76.7741	167	914	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.7513	123	914	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.7461	215	914	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	76.7331	118	914	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.7299	223	914	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.7136	138	914	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	76.7049	131	914	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	76.6966	166	914	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	76.6594	118	914	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	76.6552	198	914	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	76.6505	203	914	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.6038	155	914	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	76.5992	169	914	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.5481	153	914	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.5204	189	914	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.4914	150	914	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.4883	130	914	95	below_threshold
Halorhodospira halophila	strain=SL1	GCA_000015585.1	1053	1053	suspected-type	True	76.4822	80	914	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.4808	153	914	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	76.4416	115	914	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	76.4305	117	914	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.4003	141	914	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	76.3862	118	914	95	below_threshold
Methylotetracoccus oryzae	strain=C50C1	GCA_006175985.1	1919059	1919059	type	True	75.958	63	914	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.8846	132	914	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	75.7887	133	914	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.7685	148	914	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.6687	149	914	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:51:01,502] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33243/tc_result.tsv
[2023-03-16 17:51:01,502] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:51:01,502] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:51:01,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg273f6dee-b35e-48ce-bf8f-7fe10e48cb72/dqc_reference/checkm_data
[2023-03-16 17:51:01,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:51:01,541] [INFO] Task started: CheckM
[2023-03-16 17:51:01,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33243/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33243/checkm_input OceanDNA-b33243/checkm_result
[2023-03-16 17:51:45,838] [INFO] Task succeeded: CheckM
[2023-03-16 17:51:45,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 17:51:45,846] [INFO] ===== Completeness check finished =====
[2023-03-16 17:51:45,846] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:51:45,846] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33243/markers.fasta)
[2023-03-16 17:51:45,847] [INFO] Task started: Blastn
[2023-03-16 17:51:45,847] [INFO] Running command: blastn -query OceanDNA-b33243/markers.fasta -db /var/lib/cwl/stg273f6dee-b35e-48ce-bf8f-7fe10e48cb72/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33243/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:51:47,693] [INFO] Task succeeded: Blastn
[2023-03-16 17:51:47,695] [INFO] Selected 18 target genomes.
[2023-03-16 17:51:47,695] [INFO] Target genome list was writen to OceanDNA-b33243/target_genomes_gtdb.txt
[2023-03-16 17:51:47,707] [INFO] Task started: fastANI
[2023-03-16 17:51:47,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f272fcc-aad4-435b-a962-640e8de24f26/OceanDNA-b33243.fa --refList OceanDNA-b33243/target_genomes_gtdb.txt --output OceanDNA-b33243/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:51:57,290] [INFO] Task succeeded: fastANI
[2023-03-16 17:51:57,300] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:51:57,301] [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_011089885.1	s__XN24 sp011089885	81.7213	566	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058255.1	s__XN24 sp011058255	81.5791	551	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064545.1	s__XN24 sp011064545	80.906	523	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789885.1	s__SHZI01 sp016789885	77.3269	170	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__SHZI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709695.1	s__QUBU01 sp015709695	77.2826	170	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__QUBU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127715.1	s__PWYM01 sp007127715	77.2303	152	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PWYM01;f__PWYM01;g__PWYM01	95.0	99.45	99.43	0.90	0.89	3	-
GCA_016882265.1	s__SCUD01 sp016882265	77.114	172	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SCUD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242495.1	s__ZC4RG39 sp003242495	77.0054	143	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG39	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.9308	159	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428405.1	s__Frateuria_A sp001428405	76.8816	186	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695765.1	s__J054 sp003695765	76.8098	151	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__J054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494165.1	s__S144-34 sp015494165	76.7971	154	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377345.1	s__Thioalkalivibrio sp000377345	76.6683	115	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577365.1	s__ZC4RG20 sp017577365	76.6212	124	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__ZC4RG20	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003732545.1	s__Salinisphaera halophila	76.4618	114	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	76.4321	117	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCA_016927175.1	s__ZC4RG20 sp016927175	76.4246	139	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__ZC4RG20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117515.1	s__SKGQ01 sp007117515	76.4175	66	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__SKGQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:51:57,302] [INFO] GTDB search result was written to OceanDNA-b33243/result_gtdb.tsv
[2023-03-16 17:51:57,302] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:51:57,306] [INFO] DFAST_QC result json was written to OceanDNA-b33243/dqc_result.json
[2023-03-16 17:51:57,306] [INFO] DFAST_QC completed!
[2023-03-16 17:51:57,306] [INFO] Total running time: 0h1m44s