[2023-03-16 00:13:32,307] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:13:32,307] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:13:32,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg4266fead-554a-4c08-996d-61d4f493a184/dqc_reference
[2023-03-16 00:13:33,466] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:13:33,467] [INFO] Task started: Prodigal
[2023-03-16 00:13:33,467] [INFO] Running command: cat /var/lib/cwl/stgf5501439-7d79-4e33-9ede-427e607fe454/OceanDNA-b28146.fa | prodigal -d OceanDNA-b28146/cds.fna -a OceanDNA-b28146/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:13:49,925] [INFO] Task succeeded: Prodigal
[2023-03-16 00:13:49,925] [INFO] Task started: HMMsearch
[2023-03-16 00:13:49,925] [INFO] Running command: hmmsearch --tblout OceanDNA-b28146/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4266fead-554a-4c08-996d-61d4f493a184/dqc_reference/reference_markers.hmm OceanDNA-b28146/protein.faa > /dev/null
[2023-03-16 00:13:50,123] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:13:50,124] [INFO] Found 6/6 markers.
[2023-03-16 00:13:50,152] [INFO] Query marker FASTA was written to OceanDNA-b28146/markers.fasta
[2023-03-16 00:13:50,153] [INFO] Task started: Blastn
[2023-03-16 00:13:50,153] [INFO] Running command: blastn -query OceanDNA-b28146/markers.fasta -db /var/lib/cwl/stg4266fead-554a-4c08-996d-61d4f493a184/dqc_reference/reference_markers.fasta -out OceanDNA-b28146/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:13:50,845] [INFO] Task succeeded: Blastn
[2023-03-16 00:13:50,848] [INFO] Selected 32 target genomes.
[2023-03-16 00:13:50,848] [INFO] Target genome list was writen to OceanDNA-b28146/target_genomes.txt
[2023-03-16 00:13:50,867] [INFO] Task started: fastANI
[2023-03-16 00:13:50,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5501439-7d79-4e33-9ede-427e607fe454/OceanDNA-b28146.fa --refList OceanDNA-b28146/target_genomes.txt --output OceanDNA-b28146/fastani_result.tsv --threads 1
[2023-03-16 00:14:11,260] [INFO] Task succeeded: fastANI
[2023-03-16 00:14:11,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4266fead-554a-4c08-996d-61d4f493a184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:14:11,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4266fead-554a-4c08-996d-61d4f493a184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:14:11,278] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:14:11,278] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:14:11,279] [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
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	78.5407	242	852	95	below_threshold
Cognatishimia maritima	strain=DSM 28223	GCA_900129685.1	870908	870908	type	True	78.405	248	852	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	78.0125	192	852	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.9121	198	852	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.6742	208	852	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.6479	217	852	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	77.5322	200	852	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	77.4873	186	852	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.413	192	852	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	77.3031	158	852	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_900102795.1	1156985	1156985	type	True	77.2953	95	852	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.1667	166	852	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.149	164	852	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.1312	107	852	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	77.1306	164	852	95	below_threshold
Litoreibacter meonggei	strain=DSM 29466	GCA_003663885.1	1049199	1049199	type	True	77.0747	99	852	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	76.9658	155	852	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	76.7946	124	852	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	76.7778	122	852	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	76.7394	129	852	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6797	87	852	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	76.5014	102	852	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.4682	110	852	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	76.2733	118	852	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.1975	124	852	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	76.101	97	852	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	76.0941	73	852	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.0863	89	852	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.0863	89	852	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.0439	91	852	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	76.0368	100	852	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	75.838	98	852	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:14:11,280] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28146/tc_result.tsv
[2023-03-16 00:14:11,281] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:14:11,282] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:14:11,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4266fead-554a-4c08-996d-61d4f493a184/dqc_reference/checkm_data
[2023-03-16 00:14:11,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:14:11,292] [INFO] Task started: CheckM
[2023-03-16 00:14:11,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28146/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28146/checkm_input OceanDNA-b28146/checkm_result
[2023-03-16 00:14:55,073] [INFO] Task succeeded: CheckM
[2023-03-16 00:14:55,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:14:55,088] [INFO] ===== Completeness check finished =====
[2023-03-16 00:14:55,088] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:14:55,088] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28146/markers.fasta)
[2023-03-16 00:14:55,089] [INFO] Task started: Blastn
[2023-03-16 00:14:55,089] [INFO] Running command: blastn -query OceanDNA-b28146/markers.fasta -db /var/lib/cwl/stg4266fead-554a-4c08-996d-61d4f493a184/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28146/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:14:56,081] [INFO] Task succeeded: Blastn
[2023-03-16 00:14:56,085] [INFO] Selected 20 target genomes.
[2023-03-16 00:14:56,085] [INFO] Target genome list was writen to OceanDNA-b28146/target_genomes_gtdb.txt
[2023-03-16 00:14:56,101] [INFO] Task started: fastANI
[2023-03-16 00:14:56,101] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5501439-7d79-4e33-9ede-427e607fe454/OceanDNA-b28146.fa --refList OceanDNA-b28146/target_genomes_gtdb.txt --output OceanDNA-b28146/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:15:09,929] [INFO] Task succeeded: fastANI
[2023-03-16 00:15:09,941] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:15:09,941] [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_013215215.1	s__Cognatishimia sp013215215	99.4208	757	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017798205.1	s__Cognatishimia activa_A	90.1815	723	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458335.1	s__Cognatishimia activa	78.5241	243	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	99.97	99.97	0.99	0.99	2	-
GCF_900129685.1	s__Cognatishimia maritima	78.405	248	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	78.1513	239	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_017744095.1	s__Shimia sp017744095	77.8555	220	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	77.6488	217	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743935.1	s__Ruegeria_E sp017743935	77.4625	199	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	77.4604	186	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018678075.1	s__Epibacterium ulvae_A	77.414	156	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.1667	166	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407245.1	s__Phaeobacter piscinae	77.1433	181	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCA_001730095.1	s__Leisingera sp001730095	77.1384	169	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001518015.1	s__Epibacterium horizontis	77.1088	161	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.0942	192	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.016	165	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500245.1	s__Ruegeria_B sp010500245	76.7745	169	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142765.1	s__Roseovarius litoreus	76.7265	128	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	76.6068	119	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	76.5418	130	852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:15:09,943] [INFO] GTDB search result was written to OceanDNA-b28146/result_gtdb.tsv
[2023-03-16 00:15:09,945] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:15:09,950] [INFO] DFAST_QC result json was written to OceanDNA-b28146/dqc_result.json
[2023-03-16 00:15:09,951] [INFO] DFAST_QC completed!
[2023-03-16 00:15:09,951] [INFO] Total running time: 0h1m38s