[2023-03-18 22:17:12,671] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:17:12,672] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:17:12,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg87f092d4-ac83-4e0b-b973-fdd85df46321/dqc_reference
[2023-03-18 22:17:13,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:17:13,754] [INFO] Task started: Prodigal
[2023-03-18 22:17:13,754] [INFO] Running command: cat /var/lib/cwl/stg34a4c54e-4a2f-454f-b9ed-1e2dd8bd9bdb/OceanDNA-b28240.fa | prodigal -d OceanDNA-b28240/cds.fna -a OceanDNA-b28240/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:17:37,930] [INFO] Task succeeded: Prodigal
[2023-03-18 22:17:37,931] [INFO] Task started: HMMsearch
[2023-03-18 22:17:37,931] [INFO] Running command: hmmsearch --tblout OceanDNA-b28240/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87f092d4-ac83-4e0b-b973-fdd85df46321/dqc_reference/reference_markers.hmm OceanDNA-b28240/protein.faa > /dev/null
[2023-03-18 22:17:38,148] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:17:38,148] [INFO] Found 6/6 markers.
[2023-03-18 22:17:38,172] [INFO] Query marker FASTA was written to OceanDNA-b28240/markers.fasta
[2023-03-18 22:17:38,173] [INFO] Task started: Blastn
[2023-03-18 22:17:38,173] [INFO] Running command: blastn -query OceanDNA-b28240/markers.fasta -db /var/lib/cwl/stg87f092d4-ac83-4e0b-b973-fdd85df46321/dqc_reference/reference_markers.fasta -out OceanDNA-b28240/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:38,971] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:38,972] [INFO] Selected 27 target genomes.
[2023-03-18 22:17:38,972] [INFO] Target genome list was writen to OceanDNA-b28240/target_genomes.txt
[2023-03-18 22:17:38,990] [INFO] Task started: fastANI
[2023-03-18 22:17:38,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg34a4c54e-4a2f-454f-b9ed-1e2dd8bd9bdb/OceanDNA-b28240.fa --refList OceanDNA-b28240/target_genomes.txt --output OceanDNA-b28240/fastani_result.tsv --threads 1
[2023-03-18 22:17:57,043] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:57,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87f092d4-ac83-4e0b-b973-fdd85df46321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:17:57,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87f092d4-ac83-4e0b-b973-fdd85df46321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:17:57,059] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:17:57,059] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:17:57,059] [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
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	78.5037	477	1257	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7655	403	1257	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	77.6299	298	1257	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	77.6214	298	1257	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.5792	306	1257	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	77.5062	273	1257	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.4281	265	1257	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	77.4161	266	1257	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	77.3418	293	1257	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.3347	301	1257	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	77.3344	251	1257	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.1806	214	1257	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.174	267	1257	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.1603	250	1257	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.1424	252	1257	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	77.1252	233	1257	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	77.0975	266	1257	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	77.0835	230	1257	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.0333	290	1257	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.0325	207	1257	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.0291	234	1257	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.024	285	1257	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.9549	248	1257	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.9324	203	1257	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	76.9281	230	1257	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.9158	260	1257	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.872	213	1257	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:17:57,061] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28240/tc_result.tsv
[2023-03-18 22:17:57,062] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:17:57,062] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:17:57,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87f092d4-ac83-4e0b-b973-fdd85df46321/dqc_reference/checkm_data
[2023-03-18 22:17:57,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:17:57,075] [INFO] Task started: CheckM
[2023-03-18 22:17:57,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28240/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28240/checkm_input OceanDNA-b28240/checkm_result
[2023-03-18 22:18:57,712] [INFO] Task succeeded: CheckM
[2023-03-18 22:18:57,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:18:57,715] [INFO] ===== Completeness check finished =====
[2023-03-18 22:18:57,716] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:18:57,716] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28240/markers.fasta)
[2023-03-18 22:18:57,717] [INFO] Task started: Blastn
[2023-03-18 22:18:57,717] [INFO] Running command: blastn -query OceanDNA-b28240/markers.fasta -db /var/lib/cwl/stg87f092d4-ac83-4e0b-b973-fdd85df46321/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28240/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:18:59,176] [INFO] Task succeeded: Blastn
[2023-03-18 22:18:59,177] [INFO] Selected 30 target genomes.
[2023-03-18 22:18:59,177] [INFO] Target genome list was writen to OceanDNA-b28240/target_genomes_gtdb.txt
[2023-03-18 22:18:59,202] [INFO] Task started: fastANI
[2023-03-18 22:18:59,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg34a4c54e-4a2f-454f-b9ed-1e2dd8bd9bdb/OceanDNA-b28240.fa --refList OceanDNA-b28240/target_genomes_gtdb.txt --output OceanDNA-b28240/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:19:20,341] [INFO] Task succeeded: fastANI
[2023-03-18 22:19:20,357] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:19:20,358] [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_900184895.1	s__Flavimaricola marinus	78.5123	476	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	77.8414	353	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000435.1	s__Flavimaricola sp004000435	77.7732	402	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	-
GCF_000600975.2	s__Limimaricola hongkongensis	77.6608	295	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018402175.1	s__Yoonia sp018402175	77.6581	296	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCA_016125575.1	s__JAACUH01 sp016125575	77.6127	365	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128995.1	s__Loktanella atrilutea	77.6087	303	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	77.4603	347	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	77.4484	263	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.4091	293	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004145405.1	s__Loktanella sp004145405	77.3929	263	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	77.3619	291	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.3347	301	1257	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_003217255.1	s__Pseudoroseicyclus aestuarii	77.3343	251	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	77.3247	240	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	77.3076	322	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	77.2826	227	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	77.2736	278	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	77.2612	285	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	77.2302	289	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	77.1814	248	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016428585.1	s__Sedimentitalea sp016428585	77.1037	250	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196795.1	s__Sagittula marina	77.0568	205	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.0349	289	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002814095.1	s__Sagittula sp002814095	76.9942	278	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	76.9897	254	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	76.9499	228	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	76.869	248	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	76.8356	209	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.7308	203	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:19:20,363] [INFO] GTDB search result was written to OceanDNA-b28240/result_gtdb.tsv
[2023-03-18 22:19:20,363] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:19:20,366] [INFO] DFAST_QC result json was written to OceanDNA-b28240/dqc_result.json
[2023-03-18 22:19:20,366] [INFO] DFAST_QC completed!
[2023-03-18 22:19:20,366] [INFO] Total running time: 0h2m8s