[2023-03-18 04:54:25,331] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:54:25,331] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:54:25,332] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcf2e4ca-0717-4613-86f0-ab975510faa4/dqc_reference
[2023-03-18 04:54:26,988] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:54:26,989] [INFO] Task started: Prodigal
[2023-03-18 04:54:26,989] [INFO] Running command: cat /var/lib/cwl/stga02399c6-3db2-4312-94d7-e9d8f0e8b4fe/OceanDNA-b27579.fa | prodigal -d OceanDNA-b27579/cds.fna -a OceanDNA-b27579/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:54:43,041] [INFO] Task succeeded: Prodigal
[2023-03-18 04:54:43,042] [INFO] Task started: HMMsearch
[2023-03-18 04:54:43,042] [INFO] Running command: hmmsearch --tblout OceanDNA-b27579/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcf2e4ca-0717-4613-86f0-ab975510faa4/dqc_reference/reference_markers.hmm OceanDNA-b27579/protein.faa > /dev/null
[2023-03-18 04:54:43,229] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:54:43,230] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga02399c6-3db2-4312-94d7-e9d8f0e8b4fe/OceanDNA-b27579.fa]
[2023-03-18 04:54:43,254] [INFO] Query marker FASTA was written to OceanDNA-b27579/markers.fasta
[2023-03-18 04:54:43,255] [INFO] Task started: Blastn
[2023-03-18 04:54:43,255] [INFO] Running command: blastn -query OceanDNA-b27579/markers.fasta -db /var/lib/cwl/stgdcf2e4ca-0717-4613-86f0-ab975510faa4/dqc_reference/reference_markers.fasta -out OceanDNA-b27579/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:54:43,864] [INFO] Task succeeded: Blastn
[2023-03-18 04:54:43,865] [INFO] Selected 28 target genomes.
[2023-03-18 04:54:43,865] [INFO] Target genome list was writen to OceanDNA-b27579/target_genomes.txt
[2023-03-18 04:54:43,884] [INFO] Task started: fastANI
[2023-03-18 04:54:43,884] [INFO] Running command: fastANI --query /var/lib/cwl/stga02399c6-3db2-4312-94d7-e9d8f0e8b4fe/OceanDNA-b27579.fa --refList OceanDNA-b27579/target_genomes.txt --output OceanDNA-b27579/fastani_result.tsv --threads 1
[2023-03-18 04:55:02,654] [INFO] Task succeeded: fastANI
[2023-03-18 04:55:02,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcf2e4ca-0717-4613-86f0-ab975510faa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:55:02,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcf2e4ca-0717-4613-86f0-ab975510faa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:55:02,669] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:55:02,669] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:55:02,670] [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
Pikeienuella piscinae	strain=RR4-56	GCA_011044155.1	2748098	2748098	type	True	76.7565	190	880	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.4231	101	880	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	76.0135	88	880	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	75.9791	90	880	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	75.9787	104	880	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	75.9765	78	880	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	75.9658	76	880	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	75.8329	104	880	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	75.8212	105	880	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.8059	125	880	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.7658	114	880	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	75.7623	79	880	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	75.7523	132	880	95	below_threshold
Paracoccus chinensis	strain=CGMCC 1.7655	GCA_900102885.1	525640	525640	type	True	75.697	76	880	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	75.6131	91	880	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	75.5966	67	880	95	below_threshold
Litoreibacter arenae	strain=DSM 19593	GCA_000442275.2	491388	491388	type	True	75.574	55	880	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.5648	112	880	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.1998	73	880	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.1971	71	880	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	75.1494	59	880	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.1429	75	880	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.1382	74	880	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.0934	89	880	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.0167	78	880	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	74.9409	60	880	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:55:02,670] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27579/tc_result.tsv
[2023-03-18 04:55:02,670] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:55:02,670] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:55:02,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcf2e4ca-0717-4613-86f0-ab975510faa4/dqc_reference/checkm_data
[2023-03-18 04:55:02,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:55:02,796] [INFO] Task started: CheckM
[2023-03-18 04:55:02,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27579/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27579/checkm_input OceanDNA-b27579/checkm_result
[2023-03-18 04:55:44,893] [INFO] Task succeeded: CheckM
[2023-03-18 04:55:44,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:55:44,912] [INFO] ===== Completeness check finished =====
[2023-03-18 04:55:44,913] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:55:44,913] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27579/markers.fasta)
[2023-03-18 04:55:44,914] [INFO] Task started: Blastn
[2023-03-18 04:55:44,914] [INFO] Running command: blastn -query OceanDNA-b27579/markers.fasta -db /var/lib/cwl/stgdcf2e4ca-0717-4613-86f0-ab975510faa4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27579/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:55:45,815] [INFO] Task succeeded: Blastn
[2023-03-18 04:55:45,816] [INFO] Selected 25 target genomes.
[2023-03-18 04:55:45,816] [INFO] Target genome list was writen to OceanDNA-b27579/target_genomes_gtdb.txt
[2023-03-18 04:55:45,915] [INFO] Task started: fastANI
[2023-03-18 04:55:45,916] [INFO] Running command: fastANI --query /var/lib/cwl/stga02399c6-3db2-4312-94d7-e9d8f0e8b4fe/OceanDNA-b27579.fa --refList OceanDNA-b27579/target_genomes_gtdb.txt --output OceanDNA-b27579/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:56:05,956] [INFO] Task succeeded: fastANI
[2023-03-18 04:56:05,969] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:56:05,969] [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_011044155.1	s__Pikeienuella piscinae	76.7211	193	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pikeienuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	76.0491	123	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	75.9765	78	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015679265.1	s__MT2928 sp015679265	75.9663	105	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441615.1	s__Roseovarius atlanticus	75.9658	76	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	75.9616	91	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184745.1	s__Mangrovicoccus sp013184745	75.9123	127	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	75.912	93	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280515.1	s__Albidovulum sp002280515	75.8793	98	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	75.869	96	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	75.8133	126	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_005887635.2	s__Paroceanicella profunda	75.7425	133	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847445.1	s__Paracoccus zhejiangensis	75.7269	87	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258405.1	s__Amaricoccus sp003258405	75.7176	80	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	75.5863	110	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009904055.1	s__Rubellimicrobium sp009904055	75.5168	64	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	75.2179	54	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764485.1	s__Bosea sp011764485	75.1657	57	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	75.1494	59	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001315015.1	s__Azospirillum brasilense	75.1315	75	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCA_001556025.1	s__Bosea sp001556025	75.0454	69	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869975.1	s__JAFAZJ01 sp016869975	75.0339	60	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	75.0167	78	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-18 04:56:05,974] [INFO] GTDB search result was written to OceanDNA-b27579/result_gtdb.tsv
[2023-03-18 04:56:05,978] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:56:05,980] [INFO] DFAST_QC result json was written to OceanDNA-b27579/dqc_result.json
[2023-03-18 04:56:05,980] [INFO] DFAST_QC completed!
[2023-03-18 04:56:05,980] [INFO] Total running time: 0h1m41s