[2023-03-18 04:16:53,185] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:53,185] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:53,185] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c726e13-bfd0-4401-9519-0764b66fdb98/dqc_reference
[2023-03-18 04:16:54,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:54,336] [INFO] Task started: Prodigal
[2023-03-18 04:16:54,336] [INFO] Running command: cat /var/lib/cwl/stgf7db1655-2af7-4b04-8ef1-09ceb0fb3f8b/OceanDNA-b29389.fa | prodigal -d OceanDNA-b29389/cds.fna -a OceanDNA-b29389/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:10,324] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:10,324] [INFO] Task started: HMMsearch
[2023-03-18 04:17:10,324] [INFO] Running command: hmmsearch --tblout OceanDNA-b29389/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c726e13-bfd0-4401-9519-0764b66fdb98/dqc_reference/reference_markers.hmm OceanDNA-b29389/protein.faa > /dev/null
[2023-03-18 04:17:10,504] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:10,505] [INFO] Found 6/6 markers.
[2023-03-18 04:17:10,522] [INFO] Query marker FASTA was written to OceanDNA-b29389/markers.fasta
[2023-03-18 04:17:10,523] [INFO] Task started: Blastn
[2023-03-18 04:17:10,524] [INFO] Running command: blastn -query OceanDNA-b29389/markers.fasta -db /var/lib/cwl/stg9c726e13-bfd0-4401-9519-0764b66fdb98/dqc_reference/reference_markers.fasta -out OceanDNA-b29389/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:11,423] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:11,424] [INFO] Selected 23 target genomes.
[2023-03-18 04:17:11,424] [INFO] Target genome list was writen to OceanDNA-b29389/target_genomes.txt
[2023-03-18 04:17:11,457] [INFO] Task started: fastANI
[2023-03-18 04:17:11,457] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7db1655-2af7-4b04-8ef1-09ceb0fb3f8b/OceanDNA-b29389.fa --refList OceanDNA-b29389/target_genomes.txt --output OceanDNA-b29389/fastani_result.tsv --threads 1
[2023-03-18 04:17:28,770] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:28,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c726e13-bfd0-4401-9519-0764b66fdb98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:28,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c726e13-bfd0-4401-9519-0764b66fdb98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:28,783] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:28,783] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:17:28,784] [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
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	80.4748	574	893	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	79.5893	487	893	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	79.5841	488	893	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	79.5411	515	893	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	79.4302	501	893	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	79.3995	500	893	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.236	443	893	95	below_threshold
Jannaschia aquimarina	strain=DSM 28248	GCA_900188045.1	935700	935700	type	True	78.9317	403	893	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.8058	427	893	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	78.7177	464	893	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	78.5954	383	893	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.5062	408	893	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.2885	358	893	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	78.2406	337	893	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.12	359	893	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.0643	380	893	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.0033	306	893	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.9718	391	893	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.9457	346	893	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.8897	305	893	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.696	304	893	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.5802	329	893	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3185	242	893	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:28,784] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29389/tc_result.tsv
[2023-03-18 04:17:28,784] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:28,784] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:28,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c726e13-bfd0-4401-9519-0764b66fdb98/dqc_reference/checkm_data
[2023-03-18 04:17:28,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:28,804] [INFO] Task started: CheckM
[2023-03-18 04:17:28,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29389/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29389/checkm_input OceanDNA-b29389/checkm_result
[2023-03-18 04:18:10,373] [INFO] Task succeeded: CheckM
[2023-03-18 04:18:10,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.03%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:18:10,375] [INFO] ===== Completeness check finished =====
[2023-03-18 04:18:10,375] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:18:10,375] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29389/markers.fasta)
[2023-03-18 04:18:10,377] [INFO] Task started: Blastn
[2023-03-18 04:18:10,377] [INFO] Running command: blastn -query OceanDNA-b29389/markers.fasta -db /var/lib/cwl/stg9c726e13-bfd0-4401-9519-0764b66fdb98/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29389/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:18:12,030] [INFO] Task succeeded: Blastn
[2023-03-18 04:18:12,030] [INFO] Selected 22 target genomes.
[2023-03-18 04:18:12,031] [INFO] Target genome list was writen to OceanDNA-b29389/target_genomes_gtdb.txt
[2023-03-18 04:18:12,471] [INFO] Task started: fastANI
[2023-03-18 04:18:12,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7db1655-2af7-4b04-8ef1-09ceb0fb3f8b/OceanDNA-b29389.fa --refList OceanDNA-b29389/target_genomes_gtdb.txt --output OceanDNA-b29389/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:18:28,840] [INFO] Task succeeded: fastANI
[2023-03-18 04:18:28,852] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:18:28,853] [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_003340555.1	s__Jannaschia formosa	80.5126	570	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116765.1	s__Jannaschia seohaensis	79.6234	483	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013404595.1	s__Jannaschia marina	79.5561	513	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820245.1	s__Jannaschia sp016820245	79.5031	500	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	79.4207	502	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.2459	442	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001408515.1	s__Jannaschia seosinensis	79.162	421	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000877395.1	s__Jannaschia aquimarina	78.9229	396	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000153305.1	s__Oceanicola granulosus	78.8824	424	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	78.727	463	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	78.6179	381	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	78.6117	431	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	78.4814	406	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	78.4144	388	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	78.2698	289	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689705.1	s__HKCCE3408 sp015689705	78.2563	368	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	78.2168	394	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710275.1	s__Oceanicola sp008710275	78.2085	357	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	78.206	341	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314805.1	s__Roseicyclus sp001314805	77.9981	337	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	77.9089	304	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.5408	335	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:18:28,853] [INFO] GTDB search result was written to OceanDNA-b29389/result_gtdb.tsv
[2023-03-18 04:18:28,853] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:18:28,855] [INFO] DFAST_QC result json was written to OceanDNA-b29389/dqc_result.json
[2023-03-18 04:18:28,855] [INFO] DFAST_QC completed!
[2023-03-18 04:18:28,855] [INFO] Total running time: 0h1m36s