[2023-03-15 05:37:30,054] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:37:30,054] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:37:30,054] [INFO] DQC Reference Directory: /var/lib/cwl/stgded6e1e6-ff33-4ee0-93dd-f5ef57999b4a/dqc_reference
[2023-03-15 05:37:31,169] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:37:31,169] [INFO] Task started: Prodigal
[2023-03-15 05:37:31,169] [INFO] Running command: cat /var/lib/cwl/stg8b242c3e-5bf3-496a-906e-2be78eb9fa67/OceanDNA-b28125.fa | prodigal -d OceanDNA-b28125/cds.fna -a OceanDNA-b28125/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:37:52,755] [INFO] Task succeeded: Prodigal
[2023-03-15 05:37:52,755] [INFO] Task started: HMMsearch
[2023-03-15 05:37:52,755] [INFO] Running command: hmmsearch --tblout OceanDNA-b28125/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgded6e1e6-ff33-4ee0-93dd-f5ef57999b4a/dqc_reference/reference_markers.hmm OceanDNA-b28125/protein.faa > /dev/null
[2023-03-15 05:37:52,958] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:37:52,958] [INFO] Found 6/6 markers.
[2023-03-15 05:37:52,980] [INFO] Query marker FASTA was written to OceanDNA-b28125/markers.fasta
[2023-03-15 05:37:52,980] [INFO] Task started: Blastn
[2023-03-15 05:37:52,980] [INFO] Running command: blastn -query OceanDNA-b28125/markers.fasta -db /var/lib/cwl/stgded6e1e6-ff33-4ee0-93dd-f5ef57999b4a/dqc_reference/reference_markers.fasta -out OceanDNA-b28125/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:37:53,840] [INFO] Task succeeded: Blastn
[2023-03-15 05:37:53,840] [INFO] Selected 28 target genomes.
[2023-03-15 05:37:53,841] [INFO] Target genome list was writen to OceanDNA-b28125/target_genomes.txt
[2023-03-15 05:37:53,853] [INFO] Task started: fastANI
[2023-03-15 05:37:53,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b242c3e-5bf3-496a-906e-2be78eb9fa67/OceanDNA-b28125.fa --refList OceanDNA-b28125/target_genomes.txt --output OceanDNA-b28125/fastani_result.tsv --threads 1
[2023-03-15 05:38:13,566] [INFO] Task succeeded: fastANI
[2023-03-15 05:38:13,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgded6e1e6-ff33-4ee0-93dd-f5ef57999b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:38:13,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgded6e1e6-ff33-4ee0-93dd-f5ef57999b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:38:13,582] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 05:38:13,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 05:38:13,582] [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
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	98.2257	1108	1146	95	conclusive
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.3578	364	1146	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.3464	365	1146	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.2178	466	1146	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.0867	339	1146	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.0452	346	1146	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.9956	350	1146	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.9157	364	1146	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.9116	354	1146	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.8574	353	1146	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.8496	409	1146	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.844	308	1146	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.8232	327	1146	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.742	325	1146	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.6243	306	1146	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6137	293	1146	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	77.5331	342	1146	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.5252	336	1146	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.5222	338	1146	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.4916	301	1146	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.3805	344	1146	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.3644	350	1146	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	77.3427	293	1146	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	77.341	343	1146	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.3284	253	1146	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	77.3212	289	1146	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.3027	296	1146	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	77.1428	278	1146	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:38:13,582] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28125/tc_result.tsv
[2023-03-15 05:38:13,583] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:38:13,583] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:38:13,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgded6e1e6-ff33-4ee0-93dd-f5ef57999b4a/dqc_reference/checkm_data
[2023-03-15 05:38:13,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:38:13,651] [INFO] Task started: CheckM
[2023-03-15 05:38:13,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28125/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28125/checkm_input OceanDNA-b28125/checkm_result
[2023-03-15 05:39:07,781] [INFO] Task succeeded: CheckM
[2023-03-15 05:39:07,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:39:07,788] [INFO] ===== Completeness check finished =====
[2023-03-15 05:39:07,788] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:39:07,788] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28125/markers.fasta)
[2023-03-15 05:39:07,790] [INFO] Task started: Blastn
[2023-03-15 05:39:07,790] [INFO] Running command: blastn -query OceanDNA-b28125/markers.fasta -db /var/lib/cwl/stgded6e1e6-ff33-4ee0-93dd-f5ef57999b4a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28125/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:39:09,431] [INFO] Task succeeded: Blastn
[2023-03-15 05:39:09,433] [INFO] Selected 26 target genomes.
[2023-03-15 05:39:09,433] [INFO] Target genome list was writen to OceanDNA-b28125/target_genomes_gtdb.txt
[2023-03-15 05:39:09,460] [INFO] Task started: fastANI
[2023-03-15 05:39:09,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b242c3e-5bf3-496a-906e-2be78eb9fa67/OceanDNA-b28125.fa --refList OceanDNA-b28125/target_genomes_gtdb.txt --output OceanDNA-b28125/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:39:29,260] [INFO] Task succeeded: fastANI
[2023-03-15 05:39:29,275] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:39:29,275] [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_002504165.1	s__Pacificitalea manganoxidans	98.2257	1108	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	conclusive
GCF_018139985.1	s__JAGSOU01 sp018139985	78.5111	408	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	78.377	361	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001975705.1	s__Salipiger abyssi	78.2477	405	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	78.184	471	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_002786295.1	s__Pseudooceanicola marinus	78.0349	347	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016938875.1	s__Rhodovulum sp016938875	78.011	333	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	78.0008	404	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.8496	409	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	77.8443	325	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_000590925.1	s__Roseicyclus elongatus	77.844	308	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	77.7301	269	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363255.1	s__Roseivivax sp009363255	77.648	317	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	99.55	99.55	0.94	0.94	2	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.6154	307	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_000526275.1	s__Lutimaribacter sp000526275	77.6136	347	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359745.1	s__JACIYW01 sp014359745	77.5877	267	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACIYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.5626	326	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.5399	397	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	77.5222	338	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCA_009993005.1	s__JAACUH01 sp009993005	77.5085	311	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	-
GCA_002706605.1	s__SAT37 sp002706605	77.5022	262	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SAT37	95.0	99.85	99.85	0.95	0.95	2	-
GCF_013184745.1	s__Mangrovicoccus sp013184745	77.4971	369	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	77.4491	346	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	77.3643	350	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.3027	296	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_002119405.1	s__Fluviibacterium sp002119405	77.1829	211	1146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:39:29,277] [INFO] GTDB search result was written to OceanDNA-b28125/result_gtdb.tsv
[2023-03-15 05:39:29,278] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:39:29,282] [INFO] DFAST_QC result json was written to OceanDNA-b28125/dqc_result.json
[2023-03-15 05:39:29,282] [INFO] DFAST_QC completed!
[2023-03-15 05:39:29,282] [INFO] Total running time: 0h1m59s