[2023-03-15 19:02:29,955] [INFO] DFAST_QC pipeline started.
[2023-03-15 19:02:29,956] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 19:02:29,956] [INFO] DQC Reference Directory: /var/lib/cwl/stgaad03607-8e1d-4030-ad5e-a3860cca5514/dqc_reference
[2023-03-15 19:02:32,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 19:02:32,598] [INFO] Task started: Prodigal
[2023-03-15 19:02:32,599] [INFO] Running command: cat /var/lib/cwl/stgc4ebcc9b-c041-433a-a3f9-5ad78e72391e/OceanDNA-b28246.fa | prodigal -d OceanDNA-b28246/cds.fna -a OceanDNA-b28246/protein.faa -g 11 -q > /dev/null
[2023-03-15 19:02:45,548] [INFO] Task succeeded: Prodigal
[2023-03-15 19:02:45,549] [INFO] Task started: HMMsearch
[2023-03-15 19:02:45,549] [INFO] Running command: hmmsearch --tblout OceanDNA-b28246/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaad03607-8e1d-4030-ad5e-a3860cca5514/dqc_reference/reference_markers.hmm OceanDNA-b28246/protein.faa > /dev/null
[2023-03-15 19:02:45,726] [INFO] Task succeeded: HMMsearch
[2023-03-15 19:02:45,727] [INFO] Found 6/6 markers.
[2023-03-15 19:02:45,745] [INFO] Query marker FASTA was written to OceanDNA-b28246/markers.fasta
[2023-03-15 19:02:45,745] [INFO] Task started: Blastn
[2023-03-15 19:02:45,745] [INFO] Running command: blastn -query OceanDNA-b28246/markers.fasta -db /var/lib/cwl/stgaad03607-8e1d-4030-ad5e-a3860cca5514/dqc_reference/reference_markers.fasta -out OceanDNA-b28246/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:02:46,609] [INFO] Task succeeded: Blastn
[2023-03-15 19:02:46,610] [INFO] Selected 25 target genomes.
[2023-03-15 19:02:46,610] [INFO] Target genome list was writen to OceanDNA-b28246/target_genomes.txt
[2023-03-15 19:02:46,624] [INFO] Task started: fastANI
[2023-03-15 19:02:46,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4ebcc9b-c041-433a-a3f9-5ad78e72391e/OceanDNA-b28246.fa --refList OceanDNA-b28246/target_genomes.txt --output OceanDNA-b28246/fastani_result.tsv --threads 1
[2023-03-15 19:03:04,266] [INFO] Task succeeded: fastANI
[2023-03-15 19:03:04,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaad03607-8e1d-4030-ad5e-a3860cca5514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 19:03:04,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaad03607-8e1d-4030-ad5e-a3860cca5514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 19:03:04,281] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 19:03:04,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 19:03:04,281] [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
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.2218	386	706	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	79.1855	357	706	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	79.1157	405	706	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	79.107	358	706	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	79.0919	402	706	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	79.0369	407	706	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.9816	385	706	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	78.875	352	706	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	78.6892	343	706	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.6468	347	706	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	78.6073	345	706	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.5281	321	706	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	78.5033	313	706	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.0036	312	706	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.8933	267	706	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.8389	241	706	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.8235	267	706	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.818	279	706	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7889	281	706	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.7277	241	706	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	77.6319	277	706	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.3624	248	706	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	77.3033	209	706	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.2618	230	706	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.1509	204	706	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 19:03:04,281] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28246/tc_result.tsv
[2023-03-15 19:03:04,281] [INFO] ===== Taxonomy check completed =====
[2023-03-15 19:03:04,281] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 19:03:04,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaad03607-8e1d-4030-ad5e-a3860cca5514/dqc_reference/checkm_data
[2023-03-15 19:03:04,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 19:03:04,288] [INFO] Task started: CheckM
[2023-03-15 19:03:04,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28246/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28246/checkm_input OceanDNA-b28246/checkm_result
[2023-03-15 19:03:39,067] [INFO] Task succeeded: CheckM
[2023-03-15 19:03:39,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 19:03:39,069] [INFO] ===== Completeness check finished =====
[2023-03-15 19:03:39,069] [INFO] ===== Start GTDB Search =====
[2023-03-15 19:03:39,070] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28246/markers.fasta)
[2023-03-15 19:03:39,071] [INFO] Task started: Blastn
[2023-03-15 19:03:39,071] [INFO] Running command: blastn -query OceanDNA-b28246/markers.fasta -db /var/lib/cwl/stgaad03607-8e1d-4030-ad5e-a3860cca5514/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28246/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:03:40,751] [INFO] Task succeeded: Blastn
[2023-03-15 19:03:40,752] [INFO] Selected 25 target genomes.
[2023-03-15 19:03:40,752] [INFO] Target genome list was writen to OceanDNA-b28246/target_genomes_gtdb.txt
[2023-03-15 19:03:41,080] [INFO] Task started: fastANI
[2023-03-15 19:03:41,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4ebcc9b-c041-433a-a3f9-5ad78e72391e/OceanDNA-b28246.fa --refList OceanDNA-b28246/target_genomes_gtdb.txt --output OceanDNA-b28246/fastani_result_gtdb.tsv --threads 1
[2023-03-15 19:03:57,580] [INFO] Task succeeded: fastANI
[2023-03-15 19:03:57,594] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 19:03:57,594] [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_900102015.1	s__Limimaricola pyoseonensis	79.2476	384	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	79.1541	369	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	79.107	358	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000379485.1	s__Wenxinia marina	79.0871	402	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900141735.1	s__Wenxinia saemankumensis	78.9463	389	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	78.8878	351	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993005.1	s__JAACUH01 sp009993005	78.7707	359	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	-
GCF_000153305.1	s__Oceanicola granulosus	78.7034	377	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172345.1	s__Limimaricola soesokkakensis	78.6648	345	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000466965.1	s__Limimaricola cinnabarinus	78.584	347	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217255.1	s__Pseudoroseicyclus aestuarii	78.541	320	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110065.1	s__Loktanella fryxellensis	78.5073	312	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	78.0248	311	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172265.1	s__Roseivivax jejudonensis	77.9362	300	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	77.9239	301	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184895.1	s__Flavimaricola marinus	77.8891	297	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	77.8775	247	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000435.1	s__Flavimaricola sp004000435	77.7889	281	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	-
GCF_003072125.1	s__Roseovarius sediminicola	77.7417	240	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600335.2	s__Rubellimicrobium mesophilum	77.6204	278	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737065.1	s__Thioclava atlantica	77.5934	229	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428225.1	s__Roseovarius sp002428225	77.4743	162	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.12	96.12	0.88	0.88	2	-
GCF_000382265.1	s__Yoonia vestfoldensis	77.3507	249	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131685.1	s__Rhodobaculum sp007131685	77.2741	173	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.44	99.41	0.86	0.86	3	-
GCA_018402175.1	s__Yoonia sp018402175	77.1745	186	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 19:03:57,594] [INFO] GTDB search result was written to OceanDNA-b28246/result_gtdb.tsv
[2023-03-15 19:03:57,594] [INFO] ===== GTDB Search completed =====
[2023-03-15 19:03:57,597] [INFO] DFAST_QC result json was written to OceanDNA-b28246/dqc_result.json
[2023-03-15 19:03:57,597] [INFO] DFAST_QC completed!
[2023-03-15 19:03:57,597] [INFO] Total running time: 0h1m28s