[2023-03-14 12:19:39,508] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:19:39,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:19:39,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg99332baf-e76f-42a9-834d-afe07a7d0dae/dqc_reference
[2023-03-14 12:19:40,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:19:40,630] [INFO] Task started: Prodigal
[2023-03-14 12:19:40,630] [INFO] Running command: cat /var/lib/cwl/stg2375bb88-671c-405b-a007-77f05522ec7f/OceanDNA-b28563.fa | prodigal -d OceanDNA-b28563/cds.fna -a OceanDNA-b28563/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:20:02,209] [INFO] Task succeeded: Prodigal
[2023-03-14 12:20:02,210] [INFO] Task started: HMMsearch
[2023-03-14 12:20:02,210] [INFO] Running command: hmmsearch --tblout OceanDNA-b28563/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99332baf-e76f-42a9-834d-afe07a7d0dae/dqc_reference/reference_markers.hmm OceanDNA-b28563/protein.faa > /dev/null
[2023-03-14 12:20:02,408] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:20:02,408] [INFO] Found 6/6 markers.
[2023-03-14 12:20:02,434] [INFO] Query marker FASTA was written to OceanDNA-b28563/markers.fasta
[2023-03-14 12:20:02,435] [INFO] Task started: Blastn
[2023-03-14 12:20:02,435] [INFO] Running command: blastn -query OceanDNA-b28563/markers.fasta -db /var/lib/cwl/stg99332baf-e76f-42a9-834d-afe07a7d0dae/dqc_reference/reference_markers.fasta -out OceanDNA-b28563/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:20:03,207] [INFO] Task succeeded: Blastn
[2023-03-14 12:20:03,208] [INFO] Selected 33 target genomes.
[2023-03-14 12:20:03,209] [INFO] Target genome list was writen to OceanDNA-b28563/target_genomes.txt
[2023-03-14 12:20:03,228] [INFO] Task started: fastANI
[2023-03-14 12:20:03,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg2375bb88-671c-405b-a007-77f05522ec7f/OceanDNA-b28563.fa --refList OceanDNA-b28563/target_genomes.txt --output OceanDNA-b28563/fastani_result.tsv --threads 1
[2023-03-14 12:20:25,548] [INFO] Task succeeded: fastANI
[2023-03-14 12:20:25,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99332baf-e76f-42a9-834d-afe07a7d0dae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:20:25,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99332baf-e76f-42a9-834d-afe07a7d0dae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:20:25,565] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:20:25,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:20:25,566] [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
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.9504	362	1100	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.5941	311	1100	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.5748	311	1100	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	77.341	320	1100	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	77.2852	291	1100	95	below_threshold
Pseudooctadecabacter jejudonensis	strain=CECT 8397	GCA_900172275.1	1391910	1391910	type	True	77.2786	290	1100	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.2781	291	1100	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.254	258	1100	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	77.229	271	1100	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.1311	253	1100	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	77.1201	278	1100	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.0711	268	1100	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.9762	294	1100	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.9376	221	1100	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	76.8847	286	1100	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	76.879	285	1100	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8672	264	1100	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	76.8667	282	1100	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	76.8146	230	1100	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	76.7928	219	1100	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	76.7914	230	1100	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	76.775	236	1100	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.7726	274	1100	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	76.7471	222	1100	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.7072	224	1100	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	76.6977	203	1100	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	76.6888	205	1100	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.6878	272	1100	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	76.6244	246	1100	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.6223	254	1100	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.5014	210	1100	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.4865	204	1100	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.2502	168	1100	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:20:25,567] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28563/tc_result.tsv
[2023-03-14 12:20:25,567] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:20:25,567] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:20:25,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99332baf-e76f-42a9-834d-afe07a7d0dae/dqc_reference/checkm_data
[2023-03-14 12:20:25,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:20:25,582] [INFO] Task started: CheckM
[2023-03-14 12:20:25,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28563/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28563/checkm_input OceanDNA-b28563/checkm_result
[2023-03-14 12:21:20,423] [INFO] Task succeeded: CheckM
[2023-03-14 12:21:20,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:21:20,469] [INFO] ===== Completeness check finished =====
[2023-03-14 12:21:20,469] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:21:20,470] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28563/markers.fasta)
[2023-03-14 12:21:20,471] [INFO] Task started: Blastn
[2023-03-14 12:21:20,471] [INFO] Running command: blastn -query OceanDNA-b28563/markers.fasta -db /var/lib/cwl/stg99332baf-e76f-42a9-834d-afe07a7d0dae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28563/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:21:21,894] [INFO] Task succeeded: Blastn
[2023-03-14 12:21:21,906] [INFO] Selected 28 target genomes.
[2023-03-14 12:21:21,906] [INFO] Target genome list was writen to OceanDNA-b28563/target_genomes_gtdb.txt
[2023-03-14 12:21:21,934] [INFO] Task started: fastANI
[2023-03-14 12:21:21,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg2375bb88-671c-405b-a007-77f05522ec7f/OceanDNA-b28563.fa --refList OceanDNA-b28563/target_genomes_gtdb.txt --output OceanDNA-b28563/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:21:40,472] [INFO] Task succeeded: fastANI
[2023-03-14 12:21:40,487] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:21:40,487] [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
GCF_008065155.1	s__SW4 sp002732825	95.4362	997	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SW4	95.0	98.61	98.61	0.85	0.85	2	conclusive
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.7098	320	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859355.1	s__Yoonia sp014859355	77.6983	318	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.5941	311	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_001420005.1	s__Loktanella sp001420005	77.3951	299	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129565.1	s__Salibaculum griseiflavum	77.3503	319	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.3379	330	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.3227	297	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_900110705.1	s__Loktanella sp900110705	77.3161	283	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908505.1	s__Salibaculum sp009908505	77.1955	301	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	77.1223	254	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172365.1	s__Roseovarius gaetbuli	77.1197	277	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993005.1	s__JAACUH01 sp009993005	77.0247	307	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.9932	292	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	76.915	262	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184895.1	s__Flavimaricola marinus	76.8667	282	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017886375.1	s__Octadecabacter sp017886375	76.8026	256	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCA_018608045.1	s__Octadecabacter sp018608045	76.7877	224	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	76.7316	234	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	76.7276	224	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944755.1	s__Rhodovulum robiginosum	76.723	209	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	76.6985	204	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	76.6971	225	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	76.6515	215	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	76.6226	154	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400675.1	s__NORP181 sp002400675	76.5828	141	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__NORP181	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689645.1	s__Roseicyclus sp015689645	76.4428	206	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709085.1	s__Pseudooceanicola sp002709085	76.4124	151	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:21:40,493] [INFO] GTDB search result was written to OceanDNA-b28563/result_gtdb.tsv
[2023-03-14 12:21:40,504] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:21:40,510] [INFO] DFAST_QC result json was written to OceanDNA-b28563/dqc_result.json
[2023-03-14 12:21:40,510] [INFO] DFAST_QC completed!
[2023-03-14 12:21:40,511] [INFO] Total running time: 0h2m1s