[2023-03-17 07:01:49,598] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,598] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg66ce891e-83c3-4db4-8f92-829dc5fc9640/dqc_reference
[2023-03-17 07:01:51,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,526] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,526] [INFO] Running command: cat /var/lib/cwl/stg223d8673-b32b-4672-871a-164e70c7c278/OceanDNA-b27549.fa | prodigal -d OceanDNA-b27549/cds.fna -a OceanDNA-b27549/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:04,198] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:04,198] [INFO] Task started: HMMsearch
[2023-03-17 07:02:04,198] [INFO] Running command: hmmsearch --tblout OceanDNA-b27549/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66ce891e-83c3-4db4-8f92-829dc5fc9640/dqc_reference/reference_markers.hmm OceanDNA-b27549/protein.faa > /dev/null
[2023-03-17 07:02:04,393] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:04,394] [INFO] Found 6/6 markers.
[2023-03-17 07:02:04,416] [INFO] Query marker FASTA was written to OceanDNA-b27549/markers.fasta
[2023-03-17 07:02:04,416] [INFO] Task started: Blastn
[2023-03-17 07:02:04,416] [INFO] Running command: blastn -query OceanDNA-b27549/markers.fasta -db /var/lib/cwl/stg66ce891e-83c3-4db4-8f92-829dc5fc9640/dqc_reference/reference_markers.fasta -out OceanDNA-b27549/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:05,206] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:05,207] [INFO] Selected 31 target genomes.
[2023-03-17 07:02:05,207] [INFO] Target genome list was writen to OceanDNA-b27549/target_genomes.txt
[2023-03-17 07:02:05,222] [INFO] Task started: fastANI
[2023-03-17 07:02:05,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg223d8673-b32b-4672-871a-164e70c7c278/OceanDNA-b27549.fa --refList OceanDNA-b27549/target_genomes.txt --output OceanDNA-b27549/fastani_result.tsv --threads 1
[2023-03-17 07:02:23,430] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:23,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66ce891e-83c3-4db4-8f92-829dc5fc9640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:23,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66ce891e-83c3-4db4-8f92-829dc5fc9640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:23,447] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:23,447] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:02:23,447] [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
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.2206	105	580	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.1902	99	580	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.0876	105	580	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	77.0876	105	580	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.0667	129	580	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	77.0595	140	580	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	76.8585	114	580	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.8389	101	580	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8181	82	580	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	76.8069	97	580	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.7329	113	580	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	76.687	99	580	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	76.6702	105	580	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	76.6684	117	580	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	76.6521	98	580	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.639	102	580	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	76.6383	97	580	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.6342	103	580	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	76.6298	126	580	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.6286	133	580	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.5991	106	580	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	76.5146	109	580	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.5019	96	580	95	below_threshold
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	76.4972	69	580	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	76.4667	70	580	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	76.4574	107	580	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	76.3359	103	580	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	76.264	83	580	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.2385	92	580	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	76.1874	68	580	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	76.1874	68	580	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:02:23,448] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27549/tc_result.tsv
[2023-03-17 07:02:23,448] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:23,448] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:23,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66ce891e-83c3-4db4-8f92-829dc5fc9640/dqc_reference/checkm_data
[2023-03-17 07:02:23,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:23,454] [INFO] Task started: CheckM
[2023-03-17 07:02:23,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27549/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27549/checkm_input OceanDNA-b27549/checkm_result
[2023-03-17 07:02:59,276] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:59,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.69%
Contamintation: 1.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:59,279] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:59,280] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:59,280] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27549/markers.fasta)
[2023-03-17 07:02:59,280] [INFO] Task started: Blastn
[2023-03-17 07:02:59,280] [INFO] Running command: blastn -query OceanDNA-b27549/markers.fasta -db /var/lib/cwl/stg66ce891e-83c3-4db4-8f92-829dc5fc9640/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27549/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:03:00,709] [INFO] Task succeeded: Blastn
[2023-03-17 07:03:00,710] [INFO] Selected 29 target genomes.
[2023-03-17 07:03:00,710] [INFO] Target genome list was writen to OceanDNA-b27549/target_genomes_gtdb.txt
[2023-03-17 07:03:01,096] [INFO] Task started: fastANI
[2023-03-17 07:03:01,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg223d8673-b32b-4672-871a-164e70c7c278/OceanDNA-b27549.fa --refList OceanDNA-b27549/target_genomes_gtdb.txt --output OceanDNA-b27549/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:03:18,255] [INFO] Task succeeded: fastANI
[2023-03-17 07:03:18,271] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:03:18,271] [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_012103375.1	s__WLWX01 sp012103375	80.8801	412	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WLWX01	95.0	99.99	99.98	0.99	0.99	3	-
GCF_002797755.1	s__Brevirhabdus pacifica	77.2206	105	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_900142185.1	s__Lutimaribacter pacificus	76.9913	128	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	76.9844	146	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	76.9702	121	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.9683	115	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	76.9376	128	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	76.8585	114	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	76.8521	112	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	76.8389	101	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004000435.1	s__Flavimaricola sp004000435	76.8181	82	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.8164	140	580	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_000152625.1	s__Roseovarius nubinhibens	76.8069	97	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCA_013042605.1	s__IMCC34051 sp013042605	76.7902	97	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
GCF_900142295.1	s__Vannielia litorea	76.7317	79	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	76.7212	81	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_900110115.1	s__Palleronia pelagia	76.6684	117	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	76.6159	127	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	76.5861	91	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001730095.1	s__Leisingera sp001730095	76.562	80	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	76.531	85	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	76.5017	125	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	76.4347	89	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111315.1	s__Tranquillimonas rosea	76.4321	113	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	76.3359	103	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCA_013214635.1	s__JABSSC01 sp013214635	76.2544	67	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811755.1	s__Pararhodobacter sp017811755	76.2367	81	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663885.1	s__Litoreibacter meonggei	76.1853	91	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004751985.1	s__Rhodophyticola sp004751985	76.1683	89	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:03:18,271] [INFO] GTDB search result was written to OceanDNA-b27549/result_gtdb.tsv
[2023-03-17 07:03:18,271] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:03:18,274] [INFO] DFAST_QC result json was written to OceanDNA-b27549/dqc_result.json
[2023-03-17 07:03:18,274] [INFO] DFAST_QC completed!
[2023-03-17 07:03:18,274] [INFO] Total running time: 0h1m29s