[2023-03-17 04:15:14,729] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,729] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ef4cf31-67cf-4ac1-958b-aaa744c99071/dqc_reference
[2023-03-17 04:15:16,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,101] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,101] [INFO] Running command: cat /var/lib/cwl/stg292f4832-9530-47c1-ba1f-6528c4cd7fc8/OceanDNA-b32775.fa | prodigal -d OceanDNA-b32775/cds.fna -a OceanDNA-b32775/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:34,957] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:34,957] [INFO] Task started: HMMsearch
[2023-03-17 04:15:34,957] [INFO] Running command: hmmsearch --tblout OceanDNA-b32775/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ef4cf31-67cf-4ac1-958b-aaa744c99071/dqc_reference/reference_markers.hmm OceanDNA-b32775/protein.faa > /dev/null
[2023-03-17 04:15:35,244] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:35,244] [INFO] Found 6/6 markers.
[2023-03-17 04:15:35,267] [INFO] Query marker FASTA was written to OceanDNA-b32775/markers.fasta
[2023-03-17 04:15:35,268] [INFO] Task started: Blastn
[2023-03-17 04:15:35,268] [INFO] Running command: blastn -query OceanDNA-b32775/markers.fasta -db /var/lib/cwl/stg3ef4cf31-67cf-4ac1-958b-aaa744c99071/dqc_reference/reference_markers.fasta -out OceanDNA-b32775/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:35,952] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:35,953] [INFO] Selected 32 target genomes.
[2023-03-17 04:15:35,953] [INFO] Target genome list was writen to OceanDNA-b32775/target_genomes.txt
[2023-03-17 04:15:35,965] [INFO] Task started: fastANI
[2023-03-17 04:15:35,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg292f4832-9530-47c1-ba1f-6528c4cd7fc8/OceanDNA-b32775.fa --refList OceanDNA-b32775/target_genomes.txt --output OceanDNA-b32775/fastani_result.tsv --threads 1
[2023-03-17 04:16:02,555] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:02,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ef4cf31-67cf-4ac1-958b-aaa744c99071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:16:02,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ef4cf31-67cf-4ac1-958b-aaa744c99071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:16:02,572] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:16:02,572] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:16:02,572] [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	76.5698	98	994	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.5537	125	994	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.3959	116	994	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.3257	150	994	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.3104	143	994	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.2979	143	994	95	below_threshold
Algihabitans albus	strain=HHTR 118	GCA_003572205.1	2164067	2164067	type	True	76.1559	87	994	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.1447	136	994	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.0866	108	994	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.0699	77	994	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.052	109	994	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.015	100	994	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	76.0083	96	994	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	75.996	94	994	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.9173	76	994	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.8685	138	994	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.8685	138	994	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	75.8498	80	994	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.842	140	994	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.8169	71	994	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.8164	110	994	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.8072	123	994	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.7805	66	994	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.7758	120	994	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.7743	61	994	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	75.7561	117	994	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	75.7388	60	994	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.7341	110	994	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	75.6696	75	994	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.549	75	994	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	75.4174	54	994	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:16:02,572] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32775/tc_result.tsv
[2023-03-17 04:16:02,572] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:16:02,572] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:16:02,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ef4cf31-67cf-4ac1-958b-aaa744c99071/dqc_reference/checkm_data
[2023-03-17 04:16:02,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:16:02,578] [INFO] Task started: CheckM
[2023-03-17 04:16:02,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32775/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32775/checkm_input OceanDNA-b32775/checkm_result
[2023-03-17 04:16:50,596] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:50,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:50,599] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:50,599] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:50,599] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32775/markers.fasta)
[2023-03-17 04:16:50,599] [INFO] Task started: Blastn
[2023-03-17 04:16:50,599] [INFO] Running command: blastn -query OceanDNA-b32775/markers.fasta -db /var/lib/cwl/stg3ef4cf31-67cf-4ac1-958b-aaa744c99071/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32775/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:51,743] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:51,744] [INFO] Selected 10 target genomes.
[2023-03-17 04:16:51,744] [INFO] Target genome list was writen to OceanDNA-b32775/target_genomes_gtdb.txt
[2023-03-17 04:16:52,089] [INFO] Task started: fastANI
[2023-03-17 04:16:52,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg292f4832-9530-47c1-ba1f-6528c4cd7fc8/OceanDNA-b32775.fa --refList OceanDNA-b32775/target_genomes_gtdb.txt --output OceanDNA-b32775/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:59,135] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:59,140] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:16:59,140] [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_018667335.1	s__UBA8079 sp018667335	99.8885	964	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	conclusive
GCA_018702955.1	s__UBA8079 sp018702955	85.5511	800	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_002727315.1	s__UBA8079 sp002727315	79.2868	401	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724635.1	s__UBA8079 sp002724635	79.1955	435	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	78.586	348	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722515.1	s__UBA8079 sp002722515	77.5192	246	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666195.1	s__JABJAG01 sp018666195	77.4601	248	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699755.1	s__JABIRQ01 sp018699755	76.3902	86	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CADEGL01;f__CADEGL01;g__JABIRQ01	95.0	98.91	98.91	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:59,141] [INFO] GTDB search result was written to OceanDNA-b32775/result_gtdb.tsv
[2023-03-17 04:16:59,141] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:59,143] [INFO] DFAST_QC result json was written to OceanDNA-b32775/dqc_result.json
[2023-03-17 04:16:59,143] [INFO] DFAST_QC completed!
[2023-03-17 04:16:59,143] [INFO] Total running time: 0h1m44s