[2023-03-17 03:24:50,958] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:24:50,959] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:24:50,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e4c315e-01d1-4a61-bb3c-4b8624e2dc10/dqc_reference
[2023-03-17 03:24:52,064] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:24:52,065] [INFO] Task started: Prodigal
[2023-03-17 03:24:52,065] [INFO] Running command: cat /var/lib/cwl/stgb2be8b6d-e964-4cda-811a-7383ad781d2e/OceanDNA-b32582.fa | prodigal -d OceanDNA-b32582/cds.fna -a OceanDNA-b32582/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:25:04,568] [INFO] Task succeeded: Prodigal
[2023-03-17 03:25:04,568] [INFO] Task started: HMMsearch
[2023-03-17 03:25:04,568] [INFO] Running command: hmmsearch --tblout OceanDNA-b32582/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e4c315e-01d1-4a61-bb3c-4b8624e2dc10/dqc_reference/reference_markers.hmm OceanDNA-b32582/protein.faa > /dev/null
[2023-03-17 03:25:04,745] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:25:04,745] [INFO] Found 6/6 markers.
[2023-03-17 03:25:04,763] [INFO] Query marker FASTA was written to OceanDNA-b32582/markers.fasta
[2023-03-17 03:25:04,764] [INFO] Task started: Blastn
[2023-03-17 03:25:04,764] [INFO] Running command: blastn -query OceanDNA-b32582/markers.fasta -db /var/lib/cwl/stg5e4c315e-01d1-4a61-bb3c-4b8624e2dc10/dqc_reference/reference_markers.fasta -out OceanDNA-b32582/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:05,372] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:05,373] [INFO] Selected 38 target genomes.
[2023-03-17 03:25:05,374] [INFO] Target genome list was writen to OceanDNA-b32582/target_genomes.txt
[2023-03-17 03:25:05,396] [INFO] Task started: fastANI
[2023-03-17 03:25:05,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2be8b6d-e964-4cda-811a-7383ad781d2e/OceanDNA-b32582.fa --refList OceanDNA-b32582/target_genomes.txt --output OceanDNA-b32582/fastani_result.tsv --threads 1
[2023-03-17 03:25:35,391] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:35,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e4c315e-01d1-4a61-bb3c-4b8624e2dc10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:25:35,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e4c315e-01d1-4a61-bb3c-4b8624e2dc10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:25:35,404] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:25:35,404] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:25:35,404] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.3124	93	627	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.1154	145	627	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.0931	99	627	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.0532	92	627	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.9312	68	627	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.8327	98	627	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.8045	70	627	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	75.6697	51	627	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.6616	105	627	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.6611	105	627	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.6597	122	627	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	75.5028	58	627	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.4878	75	627	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	75.3867	67	627	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	75.3704	53	627	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	75.2563	67	627	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.2482	90	627	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	75.2288	68	627	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	75.1532	51	627	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.1454	103	627	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	75.1149	83	627	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	75.0257	62	627	95	below_threshold
Bradyrhizobium centrolobii	strain=BR 10245	GCA_001641635.1	1505087	1505087	type	True	75.0239	52	627	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:25:35,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32582/tc_result.tsv
[2023-03-17 03:25:35,407] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:25:35,407] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:25:35,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e4c315e-01d1-4a61-bb3c-4b8624e2dc10/dqc_reference/checkm_data
[2023-03-17 03:25:35,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:25:35,413] [INFO] Task started: CheckM
[2023-03-17 03:25:35,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32582/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32582/checkm_input OceanDNA-b32582/checkm_result
[2023-03-17 03:26:10,435] [INFO] Task succeeded: CheckM
[2023-03-17 03:26:10,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:26:10,509] [INFO] ===== Completeness check finished =====
[2023-03-17 03:26:10,509] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:26:10,510] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32582/markers.fasta)
[2023-03-17 03:26:10,511] [INFO] Task started: Blastn
[2023-03-17 03:26:10,511] [INFO] Running command: blastn -query OceanDNA-b32582/markers.fasta -db /var/lib/cwl/stg5e4c315e-01d1-4a61-bb3c-4b8624e2dc10/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32582/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:26:11,415] [INFO] Task succeeded: Blastn
[2023-03-17 03:26:11,416] [INFO] Selected 33 target genomes.
[2023-03-17 03:26:11,416] [INFO] Target genome list was writen to OceanDNA-b32582/target_genomes_gtdb.txt
[2023-03-17 03:26:11,554] [INFO] Task started: fastANI
[2023-03-17 03:26:11,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2be8b6d-e964-4cda-811a-7383ad781d2e/OceanDNA-b32582.fa --refList OceanDNA-b32582/target_genomes_gtdb.txt --output OceanDNA-b32582/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:26:38,117] [INFO] Task succeeded: fastANI
[2023-03-17 03:26:38,133] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:26:38,133] [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_002694075.1	s__TMED26 sp002694075	98.6262	454	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__TMED26	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003280605.1	s__TMED26 sp003280605	76.6312	97	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__TMED26	95.0	98.88	98.84	0.81	0.75	4	-
GCA_017640745.1	s__Nisaea sp017640745	76.2397	89	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.1154	145	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	76.0931	99	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699735.1	s__JABIRP01 sp018699735	76.0301	55	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JABIRP01	95.0	99.37	99.37	0.86	0.86	2	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	75.9709	142	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203465.1	s__JABMNR01 sp013203465	75.9408	99	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JABMNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426505.1	s__Nisaea denitrificans	75.9312	68	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	75.8829	130	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.8465	97	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780745.1	s__JADHLJ01 sp016780745	75.7869	80	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JADHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363235.1	s__Dongia mobilis	75.6697	51	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	75.6497	123	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308135.1	s__Tagaea sp017308135	75.6249	59	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea	95.0	97.31	97.31	0.88	0.88	2	-
GCA_013822765.1	s__SYSU-D60009 sp013822765	75.5695	63	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010725.1	s__Azospirillum lipoferum_B	75.5208	109	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	75.5175	83	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	75.5056	119	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172325.1	s__Oceanibacterium hippocampi	75.502	74	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	75.4943	96	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003233655.1	s__Azospirillum ramasamyi	75.4926	94	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	75.4318	90	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177515.1	s__Azospirillum oryzae_A	75.3306	96	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185145.1	s__Reyranella sp016185145	75.3052	80	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116095.1	s__Azospirillum sp003116095	75.2909	105	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423485.1	s__Azospirillum oleiclasticum	75.2482	90	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000429625.1	s__Azospirillum halopraeferens	75.0956	86	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:26:38,134] [INFO] GTDB search result was written to OceanDNA-b32582/result_gtdb.tsv
[2023-03-17 03:26:38,134] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:26:38,136] [INFO] DFAST_QC result json was written to OceanDNA-b32582/dqc_result.json
[2023-03-17 03:26:38,137] [INFO] DFAST_QC completed!
[2023-03-17 03:26:38,137] [INFO] Total running time: 0h1m47s