[2023-03-15 13:54:06,140] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:54:06,140] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:54:06,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg0008aa69-6e82-4310-86e4-87381ba2b6f5/dqc_reference
[2023-03-15 13:54:07,204] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:54:07,205] [INFO] Task started: Prodigal
[2023-03-15 13:54:07,205] [INFO] Running command: cat /var/lib/cwl/stg029c683d-481d-46c8-b6f5-53b4599214b1/OceanDNA-b23315.fa | prodigal -d OceanDNA-b23315/cds.fna -a OceanDNA-b23315/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:54:38,014] [INFO] Task succeeded: Prodigal
[2023-03-15 13:54:38,015] [INFO] Task started: HMMsearch
[2023-03-15 13:54:38,015] [INFO] Running command: hmmsearch --tblout OceanDNA-b23315/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0008aa69-6e82-4310-86e4-87381ba2b6f5/dqc_reference/reference_markers.hmm OceanDNA-b23315/protein.faa > /dev/null
[2023-03-15 13:54:38,260] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:54:38,261] [INFO] Found 6/6 markers.
[2023-03-15 13:54:38,321] [INFO] Query marker FASTA was written to OceanDNA-b23315/markers.fasta
[2023-03-15 13:54:38,322] [INFO] Task started: Blastn
[2023-03-15 13:54:38,322] [INFO] Running command: blastn -query OceanDNA-b23315/markers.fasta -db /var/lib/cwl/stg0008aa69-6e82-4310-86e4-87381ba2b6f5/dqc_reference/reference_markers.fasta -out OceanDNA-b23315/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:54:39,381] [INFO] Task succeeded: Blastn
[2023-03-15 13:54:39,388] [INFO] Selected 24 target genomes.
[2023-03-15 13:54:39,389] [INFO] Target genome list was writen to OceanDNA-b23315/target_genomes.txt
[2023-03-15 13:54:39,402] [INFO] Task started: fastANI
[2023-03-15 13:54:39,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg029c683d-481d-46c8-b6f5-53b4599214b1/OceanDNA-b23315.fa --refList OceanDNA-b23315/target_genomes.txt --output OceanDNA-b23315/fastani_result.tsv --threads 1
[2023-03-15 13:55:04,639] [INFO] Task succeeded: fastANI
[2023-03-15 13:55:04,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0008aa69-6e82-4310-86e4-87381ba2b6f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:55:04,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0008aa69-6e82-4310-86e4-87381ba2b6f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:55:04,653] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:55:04,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:55:04,654] [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
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.0769	534	1696	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	77.0724	477	1696	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.0606	534	1696	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	77.0595	417	1696	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	77.0561	480	1696	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.0198	312	1696	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.9914	506	1696	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.8065	396	1696	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.6863	503	1696	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.6772	460	1696	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.6772	493	1696	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.6152	448	1696	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.5694	480	1696	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5501	234	1696	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.5214	423	1696	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	76.3704	224	1696	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	76.3596	226	1696	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.2572	254	1696	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.2454	334	1696	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.2218	287	1696	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1833	302	1696	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.0611	405	1696	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.034	277	1696	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.9573	328	1696	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:55:04,656] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23315/tc_result.tsv
[2023-03-15 13:55:04,660] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:55:04,660] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:55:04,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0008aa69-6e82-4310-86e4-87381ba2b6f5/dqc_reference/checkm_data
[2023-03-15 13:55:04,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:55:04,672] [INFO] Task started: CheckM
[2023-03-15 13:55:04,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23315/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23315/checkm_input OceanDNA-b23315/checkm_result
[2023-03-15 13:56:18,875] [INFO] Task succeeded: CheckM
[2023-03-15 13:56:18,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:56:18,988] [INFO] ===== Completeness check finished =====
[2023-03-15 13:56:18,988] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:56:18,988] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23315/markers.fasta)
[2023-03-15 13:56:18,989] [INFO] Task started: Blastn
[2023-03-15 13:56:18,989] [INFO] Running command: blastn -query OceanDNA-b23315/markers.fasta -db /var/lib/cwl/stg0008aa69-6e82-4310-86e4-87381ba2b6f5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23315/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:56:21,123] [INFO] Task succeeded: Blastn
[2023-03-15 13:56:21,128] [INFO] Selected 31 target genomes.
[2023-03-15 13:56:21,128] [INFO] Target genome list was writen to OceanDNA-b23315/target_genomes_gtdb.txt
[2023-03-15 13:56:21,163] [INFO] Task started: fastANI
[2023-03-15 13:56:21,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg029c683d-481d-46c8-b6f5-53b4599214b1/OceanDNA-b23315.fa --refList OceanDNA-b23315/target_genomes_gtdb.txt --output OceanDNA-b23315/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:56:53,607] [INFO] Task succeeded: fastANI
[2023-03-15 13:56:53,625] [INFO] Found 31 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:56:53,625] [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_015232485.1	s__JADFZP01 sp015232485	77.1954	208	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_006739055.1	s__Stella vacuolata	77.156	541	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	77.1235	473	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	77.0868	534	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006738645.1	s__Stella humosa	77.076	477	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017876115.1	s__Azospirillum picis	77.003	427	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	76.9516	473	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843145.1	s__Skermanella pratensis	76.915	382	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119115.1	s__Azospirillum sp003119115	76.909	442	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_008364795.1	s__Azospirillum oryzae	76.8289	392	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCA_009377445.1	s__WHUA01 sp009377445	76.7929	326	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.7881	329	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177515.1	s__Azospirillum oryzae_A	76.7415	437	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	76.6989	498	1696	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_017876095.1	s__Azospirillum agricola	76.6961	487	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_016595245.1	s__Azospirillum sp016595245	76.6937	451	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.6805	311	1696	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_018240745.1	s__Reyranella sp018240745	76.6744	413	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.6639	281	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.6456	202	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116035.1	s__Azospirillum sp003116035	76.6291	428	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	76.6236	461	1696	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_014644455.1	s__Caldovatus sediminis	76.5941	459	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938675.2	s__Inquilinus sp005938675	76.5777	486	1696	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_000429625.1	s__Azospirillum halopraeferens	76.5414	419	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	76.5372	486	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.4817	284	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694025.1	s__SHVZ01 sp009694025	76.4249	247	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.401	318	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	76.2976	193	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195115.1	s__JACQAI01 sp016195115	76.1077	329	1696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Elsterales;f__Elsteraceae;g__JACQAI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:56:53,634] [INFO] GTDB search result was written to OceanDNA-b23315/result_gtdb.tsv
[2023-03-15 13:56:53,645] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:56:53,657] [INFO] DFAST_QC result json was written to OceanDNA-b23315/dqc_result.json
[2023-03-15 13:56:53,657] [INFO] DFAST_QC completed!
[2023-03-15 13:56:53,657] [INFO] Total running time: 0h2m48s