[2023-03-18 03:45:10,276] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg848a8eac-8d97-4178-9a91-6c00156dddcb/dqc_reference
[2023-03-18 03:45:12,141] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,142] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,142] [INFO] Running command: cat /var/lib/cwl/stg2cde9225-70fc-4983-b790-f0452d634eef/OceanDNA-b24117.fa | prodigal -d OceanDNA-b24117/cds.fna -a OceanDNA-b24117/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:35,161] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:35,161] [INFO] Task started: HMMsearch
[2023-03-18 03:45:35,161] [INFO] Running command: hmmsearch --tblout OceanDNA-b24117/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg848a8eac-8d97-4178-9a91-6c00156dddcb/dqc_reference/reference_markers.hmm OceanDNA-b24117/protein.faa > /dev/null
[2023-03-18 03:45:35,401] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:35,402] [INFO] Found 6/6 markers.
[2023-03-18 03:45:35,429] [INFO] Query marker FASTA was written to OceanDNA-b24117/markers.fasta
[2023-03-18 03:45:35,429] [INFO] Task started: Blastn
[2023-03-18 03:45:35,430] [INFO] Running command: blastn -query OceanDNA-b24117/markers.fasta -db /var/lib/cwl/stg848a8eac-8d97-4178-9a91-6c00156dddcb/dqc_reference/reference_markers.fasta -out OceanDNA-b24117/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:36,200] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:36,201] [INFO] Selected 34 target genomes.
[2023-03-18 03:45:36,201] [INFO] Target genome list was writen to OceanDNA-b24117/target_genomes.txt
[2023-03-18 03:45:36,222] [INFO] Task started: fastANI
[2023-03-18 03:45:36,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cde9225-70fc-4983-b790-f0452d634eef/OceanDNA-b24117.fa --refList OceanDNA-b24117/target_genomes.txt --output OceanDNA-b24117/fastani_result.tsv --threads 1
[2023-03-18 03:46:03,035] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:03,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg848a8eac-8d97-4178-9a91-6c00156dddcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:46:03,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg848a8eac-8d97-4178-9a91-6c00156dddcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:46:03,048] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:46:03,048] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:46:03,048] [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
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.8972	65	1253	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.7971	73	1253	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.7817	69	1253	95	below_threshold
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	75.753	70	1253	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.704	64	1253	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.609	82	1253	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.5943	77	1253	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.5754	79	1253	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	75.5641	67	1253	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.564	64	1253	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.5108	65	1253	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.4981	64	1253	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	75.4624	50	1253	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	75.4488	64	1253	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	75.4453	56	1253	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.4075	79	1253	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	75.2991	54	1253	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=RIPI110	GCA_002119765.1	1235591	1235591	type	True	75.2773	53	1253	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=CECT 8374	GCA_003610435.1	1235591	1235591	type	True	75.2642	54	1253	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.1679	69	1253	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.1679	69	1253	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:46:03,048] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24117/tc_result.tsv
[2023-03-18 03:46:03,048] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:46:03,048] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:46:03,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg848a8eac-8d97-4178-9a91-6c00156dddcb/dqc_reference/checkm_data
[2023-03-18 03:46:03,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:46:03,115] [INFO] Task started: CheckM
[2023-03-18 03:46:03,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24117/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24117/checkm_input OceanDNA-b24117/checkm_result
[2023-03-18 03:47:00,019] [INFO] Task succeeded: CheckM
[2023-03-18 03:47:00,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:47:00,023] [INFO] ===== Completeness check finished =====
[2023-03-18 03:47:00,023] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:47:00,023] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24117/markers.fasta)
[2023-03-18 03:47:00,024] [INFO] Task started: Blastn
[2023-03-18 03:47:00,025] [INFO] Running command: blastn -query OceanDNA-b24117/markers.fasta -db /var/lib/cwl/stg848a8eac-8d97-4178-9a91-6c00156dddcb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24117/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:47:01,436] [INFO] Task succeeded: Blastn
[2023-03-18 03:47:01,438] [INFO] Selected 23 target genomes.
[2023-03-18 03:47:01,438] [INFO] Target genome list was writen to OceanDNA-b24117/target_genomes_gtdb.txt
[2023-03-18 03:47:01,735] [INFO] Task started: fastANI
[2023-03-18 03:47:01,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cde9225-70fc-4983-b790-f0452d634eef/OceanDNA-b24117.fa --refList OceanDNA-b24117/target_genomes_gtdb.txt --output OceanDNA-b24117/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:47:17,051] [INFO] Task succeeded: fastANI
[2023-03-18 03:47:17,060] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:47:17,060] [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_905479125.1	s__UBA830 sp905479125	99.2526	906	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	conclusive
GCA_905181725.1	s__UBA830 sp905181725	82.0917	753	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689465.1	s__UBA830 sp002689465	78.4597	166	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471575.1	s__UBA830 sp002471575	77.2324	298	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	-
GCA_009377375.1	s__WHUE01 sp009377375	76.0855	140	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	75.8042	95	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	75.7237	54	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	75.714	67	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241025.1	s__Rhizomicrobium sp018241025	75.6434	52	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828515.1	s__CAIKMD01 sp903828515	75.5963	77	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.99	99.96	1.00	0.99	5	-
GCA_004297265.1	s__Reyranella sp004297265	75.5113	56	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129325.1	s__Kaistia soli	75.4624	50	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	75.4488	64	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002119765.1	s__Pseudorhodoplanes sinuspersici	75.3131	54	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009649675.1	s__HT1-32 sp009649675	75.2716	52	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__HT1-32;g__HT1-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766005.1	s__Bradyrhizobium sp009766005	75.0368	63	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:47:17,061] [INFO] GTDB search result was written to OceanDNA-b24117/result_gtdb.tsv
[2023-03-18 03:47:17,061] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:47:17,063] [INFO] DFAST_QC result json was written to OceanDNA-b24117/dqc_result.json
[2023-03-18 03:47:17,063] [INFO] DFAST_QC completed!
[2023-03-18 03:47:17,063] [INFO] Total running time: 0h2m7s