[2023-03-19 02:05:11,578] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6bd391f-ff48-4cf4-98cf-168162170c1a/dqc_reference
[2023-03-19 02:05:13,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,263] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,263] [INFO] Running command: cat /var/lib/cwl/stg227eeaed-9de6-4eca-b758-6e5c1b83b6bb/OceanDNA-b31002.fa | prodigal -d OceanDNA-b31002/cds.fna -a OceanDNA-b31002/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:34,202] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:34,203] [INFO] Task started: HMMsearch
[2023-03-19 02:05:34,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b31002/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6bd391f-ff48-4cf4-98cf-168162170c1a/dqc_reference/reference_markers.hmm OceanDNA-b31002/protein.faa > /dev/null
[2023-03-19 02:05:34,456] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:34,456] [INFO] Found 6/6 markers.
[2023-03-19 02:05:34,478] [INFO] Query marker FASTA was written to OceanDNA-b31002/markers.fasta
[2023-03-19 02:05:34,479] [INFO] Task started: Blastn
[2023-03-19 02:05:34,479] [INFO] Running command: blastn -query OceanDNA-b31002/markers.fasta -db /var/lib/cwl/stgb6bd391f-ff48-4cf4-98cf-168162170c1a/dqc_reference/reference_markers.fasta -out OceanDNA-b31002/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:35,255] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:35,256] [INFO] Selected 37 target genomes.
[2023-03-19 02:05:35,257] [INFO] Target genome list was writen to OceanDNA-b31002/target_genomes.txt
[2023-03-19 02:05:35,275] [INFO] Task started: fastANI
[2023-03-19 02:05:35,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg227eeaed-9de6-4eca-b758-6e5c1b83b6bb/OceanDNA-b31002.fa --refList OceanDNA-b31002/target_genomes.txt --output OceanDNA-b31002/fastani_result.tsv --threads 1
[2023-03-19 02:06:05,539] [INFO] Task succeeded: fastANI
[2023-03-19 02:06:05,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6bd391f-ff48-4cf4-98cf-168162170c1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:06:05,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6bd391f-ff48-4cf4-98cf-168162170c1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:06:05,558] [INFO] Found 36 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:06:05,558] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:06:05,558] [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
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.9796	143	1135	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.823	131	1135	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.7426	149	1135	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.7046	143	1135	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.6298	137	1135	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.624	178	1135	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.6002	140	1135	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.4701	140	1135	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.4531	140	1135	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.4333	138	1135	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.4231	133	1135	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.3874	163	1135	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3713	183	1135	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.3482	152	1135	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.3391	152	1135	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.3126	159	1135	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.2774	148	1135	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.2716	119	1135	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.2573	150	1135	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.2374	156	1135	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	76.1675	158	1135	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	76.0669	135	1135	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.06	133	1135	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	76.044	108	1135	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.9904	174	1135	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	75.9809	92	1135	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.936	124	1135	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.8917	140	1135	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.8905	85	1135	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.7878	158	1135	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	75.725	79	1135	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	75.7147	74	1135	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	75.698	82	1135	95	below_threshold
Bradyrhizobium ivorense	strain=CI-1B	GCA_900696085.2	2511166	2511166	type	True	75.6946	119	1135	95	below_threshold
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	75.6856	77	1135	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	75.6496	73	1135	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:06:05,559] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31002/tc_result.tsv
[2023-03-19 02:06:05,559] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:06:05,559] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:06:05,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6bd391f-ff48-4cf4-98cf-168162170c1a/dqc_reference/checkm_data
[2023-03-19 02:06:05,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:06:05,565] [INFO] Task started: CheckM
[2023-03-19 02:06:05,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31002/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31002/checkm_input OceanDNA-b31002/checkm_result
[2023-03-19 02:06:57,664] [INFO] Task succeeded: CheckM
[2023-03-19 02:06:57,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:06:57,667] [INFO] ===== Completeness check finished =====
[2023-03-19 02:06:57,667] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:06:57,667] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31002/markers.fasta)
[2023-03-19 02:06:57,668] [INFO] Task started: Blastn
[2023-03-19 02:06:57,668] [INFO] Running command: blastn -query OceanDNA-b31002/markers.fasta -db /var/lib/cwl/stgb6bd391f-ff48-4cf4-98cf-168162170c1a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31002/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:06:58,932] [INFO] Task succeeded: Blastn
[2023-03-19 02:06:58,933] [INFO] Selected 8 target genomes.
[2023-03-19 02:06:58,933] [INFO] Target genome list was writen to OceanDNA-b31002/target_genomes_gtdb.txt
[2023-03-19 02:06:59,116] [INFO] Task started: fastANI
[2023-03-19 02:06:59,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg227eeaed-9de6-4eca-b758-6e5c1b83b6bb/OceanDNA-b31002.fa --refList OceanDNA-b31002/target_genomes_gtdb.txt --output OceanDNA-b31002/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:07:06,127] [INFO] Task succeeded: fastANI
[2023-03-19 02:07:06,133] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:07:06,133] [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_002433335.1	s__UBA1479 sp002433335	99.6511	945	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002696205.1	s__UBA1479 sp002696205	81.99	692	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325375.1	s__UBA1479 sp002325375	81.6796	808	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_002706405.1	s__UBA1479 sp002706405	81.4924	701	1135	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_002781745.1	s__UBA1479 sp002781745	81.165	671	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776525.1	s__JADHTD01 sp016776525	76.3155	84	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JADHTD01;g__JADHTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240745.1	s__Reyranella sp018240745	75.6981	119	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900696085.1	s__Bradyrhizobium ivorense	75.6862	122	1135	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.20	96.86	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-19 02:07:06,133] [INFO] GTDB search result was written to OceanDNA-b31002/result_gtdb.tsv
[2023-03-19 02:07:06,133] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:07:06,135] [INFO] DFAST_QC result json was written to OceanDNA-b31002/dqc_result.json
[2023-03-19 02:07:06,135] [INFO] DFAST_QC completed!
[2023-03-19 02:07:06,136] [INFO] Total running time: 0h1m55s