[2023-03-18 20:40:39,434] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f35d008-dc88-46c8-a19e-c2cd86b03acd/dqc_reference
[2023-03-18 20:40:41,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,210] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,210] [INFO] Running command: cat /var/lib/cwl/stg383e8a71-5ec2-4b30-ac35-a7d285cd6acb/OceanDNA-b27573.fa | prodigal -d OceanDNA-b27573/cds.fna -a OceanDNA-b27573/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:41:01,521] [INFO] Task succeeded: Prodigal
[2023-03-18 20:41:01,522] [INFO] Task started: HMMsearch
[2023-03-18 20:41:01,522] [INFO] Running command: hmmsearch --tblout OceanDNA-b27573/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f35d008-dc88-46c8-a19e-c2cd86b03acd/dqc_reference/reference_markers.hmm OceanDNA-b27573/protein.faa > /dev/null
[2023-03-18 20:41:01,721] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:41:01,721] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg383e8a71-5ec2-4b30-ac35-a7d285cd6acb/OceanDNA-b27573.fa]
[2023-03-18 20:41:01,744] [INFO] Query marker FASTA was written to OceanDNA-b27573/markers.fasta
[2023-03-18 20:41:01,744] [INFO] Task started: Blastn
[2023-03-18 20:41:01,745] [INFO] Running command: blastn -query OceanDNA-b27573/markers.fasta -db /var/lib/cwl/stg0f35d008-dc88-46c8-a19e-c2cd86b03acd/dqc_reference/reference_markers.fasta -out OceanDNA-b27573/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:02,551] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:02,552] [INFO] Selected 24 target genomes.
[2023-03-18 20:41:02,553] [INFO] Target genome list was writen to OceanDNA-b27573/target_genomes.txt
[2023-03-18 20:41:02,567] [INFO] Task started: fastANI
[2023-03-18 20:41:02,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg383e8a71-5ec2-4b30-ac35-a7d285cd6acb/OceanDNA-b27573.fa --refList OceanDNA-b27573/target_genomes.txt --output OceanDNA-b27573/fastani_result.tsv --threads 1
[2023-03-18 20:41:20,642] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:20,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f35d008-dc88-46c8-a19e-c2cd86b03acd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:20,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f35d008-dc88-46c8-a19e-c2cd86b03acd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:20,656] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:20,656] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:20,656] [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
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.3771	263	1181	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.3263	345	1181	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	77.321	357	1181	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	77.1437	361	1181	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.0826	323	1181	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	77.0474	413	1181	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	77.0312	362	1181	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	77.0086	268	1181	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	76.9104	314	1181	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	76.8735	271	1181	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	76.8086	240	1181	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.7353	245	1181	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	76.7204	232	1181	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	76.659	252	1181	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	76.6547	252	1181	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	76.5612	194	1181	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	76.1722	224	1181	95	below_threshold
Celeribacter indicus	strain=P73	GCA_900106965.1	1208324	1208324	type	True	76.1602	223	1181	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.1401	150	1181	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	76.1092	133	1181	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	76.0979	135	1181	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	75.9995	186	1181	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	75.9069	215	1181	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.7462	239	1181	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:20,657] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27573/tc_result.tsv
[2023-03-18 20:41:20,657] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:20,657] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:20,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f35d008-dc88-46c8-a19e-c2cd86b03acd/dqc_reference/checkm_data
[2023-03-18 20:41:20,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:20,662] [INFO] Task started: CheckM
[2023-03-18 20:41:20,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27573/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27573/checkm_input OceanDNA-b27573/checkm_result
[2023-03-18 20:42:10,612] [INFO] Task succeeded: CheckM
[2023-03-18 20:42:10,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:42:10,615] [INFO] ===== Completeness check finished =====
[2023-03-18 20:42:10,615] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:42:10,615] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27573/markers.fasta)
[2023-03-18 20:42:10,615] [INFO] Task started: Blastn
[2023-03-18 20:42:10,615] [INFO] Running command: blastn -query OceanDNA-b27573/markers.fasta -db /var/lib/cwl/stg0f35d008-dc88-46c8-a19e-c2cd86b03acd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27573/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:42:12,185] [INFO] Task succeeded: Blastn
[2023-03-18 20:42:12,186] [INFO] Selected 24 target genomes.
[2023-03-18 20:42:12,186] [INFO] Target genome list was writen to OceanDNA-b27573/target_genomes_gtdb.txt
[2023-03-18 20:42:12,211] [INFO] Task started: fastANI
[2023-03-18 20:42:12,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg383e8a71-5ec2-4b30-ac35-a7d285cd6acb/OceanDNA-b27573.fa --refList OceanDNA-b27573/target_genomes_gtdb.txt --output OceanDNA-b27573/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:30,585] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:30,598] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:42:30,598] [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_013093415.1	s__Halovulum dunhuangense	77.3445	266	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	77.3435	343	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	77.3195	351	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	77.3186	357	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCA_003250135.1	s__SZUA-547 sp003250135	77.1696	152	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-547	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695135.1	s__J013 sp003695135	77.1348	231	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__J013	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	77.1287	233	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	77.1079	320	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107585.1	s__Rubrimonas cliftonensis	77.0604	358	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.0545	381	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113695.1	s__Albimonas pacifica	77.0344	415	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	76.9928	334	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184745.1	s__Mangrovicoccus sp013184745	76.9466	340	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056725.1	s__Mangrovicoccus ximenensis	76.9086	315	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	76.727	246	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995835.1	s__Amaricoccus sp017995835	76.7256	249	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	76.7106	233	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	76.6728	250	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017303295.1	s__Pararhodobacter sp017303295	76.5748	209	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839845.1	s__Pseudolabrys sp903839845	76.1314	134	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.70	99.58	0.91	0.88	17	-
GCA_002708825.1	s__Zhengella sp002708825	76.1189	145	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Zhengella	95.0	99.96	99.96	0.93	0.93	2	-
GCF_016629525.1	s__Kaistia sp016629525	76.0802	229	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083525.1	s__SG-bin9 sp002083525	76.0207	112	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__SG-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034915.1	s__Mesorhizobium helmanticense	76.0079	185	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.01	95.01	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:30,599] [INFO] GTDB search result was written to OceanDNA-b27573/result_gtdb.tsv
[2023-03-18 20:42:30,599] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:30,601] [INFO] DFAST_QC result json was written to OceanDNA-b27573/dqc_result.json
[2023-03-18 20:42:30,601] [INFO] DFAST_QC completed!
[2023-03-18 20:42:30,601] [INFO] Total running time: 0h1m51s