[2023-03-18 08:55:50,585] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,585] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ab8a98c-c442-488f-93a1-b732d9cb3136/dqc_reference
[2023-03-18 08:55:51,718] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,718] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,718] [INFO] Running command: cat /var/lib/cwl/stgbf4ea357-03bd-427e-b650-06d63f3a70c8/OceanDNA-b30738.fa | prodigal -d OceanDNA-b30738/cds.fna -a OceanDNA-b30738/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:10,014] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:10,014] [INFO] Task started: HMMsearch
[2023-03-18 08:56:10,014] [INFO] Running command: hmmsearch --tblout OceanDNA-b30738/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ab8a98c-c442-488f-93a1-b732d9cb3136/dqc_reference/reference_markers.hmm OceanDNA-b30738/protein.faa > /dev/null
[2023-03-18 08:56:10,227] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:10,227] [INFO] Found 6/6 markers.
[2023-03-18 08:56:10,247] [INFO] Query marker FASTA was written to OceanDNA-b30738/markers.fasta
[2023-03-18 08:56:10,249] [INFO] Task started: Blastn
[2023-03-18 08:56:10,249] [INFO] Running command: blastn -query OceanDNA-b30738/markers.fasta -db /var/lib/cwl/stg9ab8a98c-c442-488f-93a1-b732d9cb3136/dqc_reference/reference_markers.fasta -out OceanDNA-b30738/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:10,927] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:10,928] [INFO] Selected 33 target genomes.
[2023-03-18 08:56:10,928] [INFO] Target genome list was writen to OceanDNA-b30738/target_genomes.txt
[2023-03-18 08:56:10,953] [INFO] Task started: fastANI
[2023-03-18 08:56:10,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf4ea357-03bd-427e-b650-06d63f3a70c8/OceanDNA-b30738.fa --refList OceanDNA-b30738/target_genomes.txt --output OceanDNA-b30738/fastani_result.tsv --threads 1
[2023-03-18 08:56:34,418] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:34,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ab8a98c-c442-488f-93a1-b732d9cb3136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:34,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ab8a98c-c442-488f-93a1-b732d9cb3136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:34,430] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:34,430] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:56:34,430] [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
Magnetovibrio blakemorei	strain=MV-1	GCA_001746755.1	28181	28181	type	True	76.3986	80	965	95	below_threshold
Varunaivibrio sulfuroxidans	strain=DSM 101688	GCA_004341725.1	1773489	1773489	type	True	76.382	105	965	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.0791	101	965	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	75.9291	68	965	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.9143	95	965	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.8844	90	965	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.8543	101	965	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	75.7317	91	965	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.6741	96	965	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.6601	122	965	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.6456	98	965	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	75.5244	112	965	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	75.5095	96	965	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	75.4811	50	965	95	below_threshold
Niveispirillum irakense	strain=DSM 11586	GCA_000429645.1	34011	34011	type	True	75.478	56	965	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	75.4581	53	965	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	75.4581	53	965	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.4386	105	965	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.3263	55	965	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:56:34,430] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30738/tc_result.tsv
[2023-03-18 08:56:34,430] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:34,430] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:34,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ab8a98c-c442-488f-93a1-b732d9cb3136/dqc_reference/checkm_data
[2023-03-18 08:56:34,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:34,436] [INFO] Task started: CheckM
[2023-03-18 08:56:34,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30738/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30738/checkm_input OceanDNA-b30738/checkm_result
[2023-03-18 08:57:21,461] [INFO] Task succeeded: CheckM
[2023-03-18 08:57:21,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:57:21,467] [INFO] ===== Completeness check finished =====
[2023-03-18 08:57:21,467] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:57:21,468] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30738/markers.fasta)
[2023-03-18 08:57:21,469] [INFO] Task started: Blastn
[2023-03-18 08:57:21,469] [INFO] Running command: blastn -query OceanDNA-b30738/markers.fasta -db /var/lib/cwl/stg9ab8a98c-c442-488f-93a1-b732d9cb3136/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30738/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:57:22,753] [INFO] Task succeeded: Blastn
[2023-03-18 08:57:22,754] [INFO] Selected 20 target genomes.
[2023-03-18 08:57:22,754] [INFO] Target genome list was writen to OceanDNA-b30738/target_genomes_gtdb.txt
[2023-03-18 08:57:22,770] [INFO] Task started: fastANI
[2023-03-18 08:57:22,770] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf4ea357-03bd-427e-b650-06d63f3a70c8/OceanDNA-b30738.fa --refList OceanDNA-b30738/target_genomes_gtdb.txt --output OceanDNA-b30738/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:57:34,015] [INFO] Task succeeded: fastANI
[2023-03-18 08:57:34,026] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:57:34,026] [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_013204045.1	s__JABMOQ01 sp013204045	78.0559	235	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABMOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382375.1	s__JACNJU01 sp014382375	77.3366	227	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JACNJU01	95.0	99.73	99.73	0.94	0.94	2	-
GCA_018671895.1	s__JABHGV01 sp018671895	77.2903	216	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABHGV01	95.0	99.83	99.79	0.94	0.93	6	-
GCA_018662005.1	s__JACNJU01 sp018662005	77.2258	226	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JACNJU01	95.0	99.95	99.92	0.95	0.94	5	-
GCA_016776705.1	s__JADHSW01 sp016776705	77.1688	145	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JADHSW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776525.1	s__JADHTD01 sp016776525	76.8036	117	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JADHTD01;g__JADHTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763915.1	s__Casp-alpha2 sp016763915	76.5383	85	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	76.411	159	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_002706405.1	s__UBA1479 sp002706405	76.3101	124	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	76.1577	130	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_001830425.1	s__2-02-FULL-58-16 sp001830425	76.0353	72	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__2-02-FULL-58-16	95.0	99.96	99.96	0.97	0.97	2	-
GCA_016187325.1	s__JACPJY01 sp016187325	75.9357	78	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	75.7993	96	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	75.7713	92	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	75.7215	99	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435715.1	s__Magnetospirillum sp002435715	75.7212	98	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898825.1	s__Magnetospirillum sp001898825	75.6767	129	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	95.98	95.98	0.88	0.88	2	-
GCA_013003675.1	s__JABDIP01 sp013003675	75.6271	61	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927615.1	s__BOG-933 sp903927615	75.568	54	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__BOG-933	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	75.4261	61	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:57:34,027] [INFO] GTDB search result was written to OceanDNA-b30738/result_gtdb.tsv
[2023-03-18 08:57:34,027] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:57:34,029] [INFO] DFAST_QC result json was written to OceanDNA-b30738/dqc_result.json
[2023-03-18 08:57:34,029] [INFO] DFAST_QC completed!
[2023-03-18 08:57:34,029] [INFO] Total running time: 0h1m43s