[2023-03-18 10:27:56,387] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:27:56,389] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:27:56,389] [INFO] DQC Reference Directory: /var/lib/cwl/stgf713c6e7-a172-4157-8d3f-17bbd6fe0f0d/dqc_reference
[2023-03-18 10:27:57,494] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:27:57,494] [INFO] Task started: Prodigal
[2023-03-18 10:27:57,494] [INFO] Running command: cat /var/lib/cwl/stgc8464d1b-8b7f-49d5-9016-e92d922f15b8/OceanDNA-b27620.fa | prodigal -d OceanDNA-b27620/cds.fna -a OceanDNA-b27620/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:28:15,899] [INFO] Task succeeded: Prodigal
[2023-03-18 10:28:15,900] [INFO] Task started: HMMsearch
[2023-03-18 10:28:15,900] [INFO] Running command: hmmsearch --tblout OceanDNA-b27620/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf713c6e7-a172-4157-8d3f-17bbd6fe0f0d/dqc_reference/reference_markers.hmm OceanDNA-b27620/protein.faa > /dev/null
[2023-03-18 10:28:16,136] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:28:16,137] [INFO] Found 6/6 markers.
[2023-03-18 10:28:16,218] [INFO] Query marker FASTA was written to OceanDNA-b27620/markers.fasta
[2023-03-18 10:28:16,219] [INFO] Task started: Blastn
[2023-03-18 10:28:16,219] [INFO] Running command: blastn -query OceanDNA-b27620/markers.fasta -db /var/lib/cwl/stgf713c6e7-a172-4157-8d3f-17bbd6fe0f0d/dqc_reference/reference_markers.fasta -out OceanDNA-b27620/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:28:17,101] [INFO] Task succeeded: Blastn
[2023-03-18 10:28:17,120] [INFO] Selected 20 target genomes.
[2023-03-18 10:28:17,121] [INFO] Target genome list was writen to OceanDNA-b27620/target_genomes.txt
[2023-03-18 10:28:17,133] [INFO] Task started: fastANI
[2023-03-18 10:28:17,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8464d1b-8b7f-49d5-9016-e92d922f15b8/OceanDNA-b27620.fa --refList OceanDNA-b27620/target_genomes.txt --output OceanDNA-b27620/fastani_result.tsv --threads 1
[2023-03-18 10:28:33,747] [INFO] Task succeeded: fastANI
[2023-03-18 10:28:33,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf713c6e7-a172-4157-8d3f-17bbd6fe0f0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:28:33,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf713c6e7-a172-4157-8d3f-17bbd6fe0f0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:28:33,760] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 10:28:33,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 10:28:33,760] [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
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	96.9803	974	1018	95	conclusive
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	81.5098	730	1018	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.243	410	1018	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	77.6319	396	1018	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.4569	360	1018	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.3922	259	1018	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	77.2406	232	1018	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	77.2082	234	1018	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	77.1765	296	1018	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	77.0873	360	1018	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.9392	222	1018	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	76.9028	314	1018	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	76.9	280	1018	95	below_threshold
Pikeienuella piscinae	strain=RR4-56	GCA_011044155.1	2748098	2748098	type	True	76.721	240	1018	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.7147	278	1018	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.7125	211	1018	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.6374	312	1018	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.3213	168	1018	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.7749	228	1018	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.2947	179	1018	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:28:33,767] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27620/tc_result.tsv
[2023-03-18 10:28:33,782] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:28:33,782] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:28:33,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf713c6e7-a172-4157-8d3f-17bbd6fe0f0d/dqc_reference/checkm_data
[2023-03-18 10:28:33,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:28:33,791] [INFO] Task started: CheckM
[2023-03-18 10:28:33,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27620/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27620/checkm_input OceanDNA-b27620/checkm_result
[2023-03-18 10:29:20,534] [INFO] Task succeeded: CheckM
[2023-03-18 10:29:20,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:29:20,598] [INFO] ===== Completeness check finished =====
[2023-03-18 10:29:20,598] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:29:20,598] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27620/markers.fasta)
[2023-03-18 10:29:20,599] [INFO] Task started: Blastn
[2023-03-18 10:29:20,599] [INFO] Running command: blastn -query OceanDNA-b27620/markers.fasta -db /var/lib/cwl/stgf713c6e7-a172-4157-8d3f-17bbd6fe0f0d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27620/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:29:22,322] [INFO] Task succeeded: Blastn
[2023-03-18 10:29:22,342] [INFO] Selected 15 target genomes.
[2023-03-18 10:29:22,342] [INFO] Target genome list was writen to OceanDNA-b27620/target_genomes_gtdb.txt
[2023-03-18 10:29:22,486] [INFO] Task started: fastANI
[2023-03-18 10:29:22,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8464d1b-8b7f-49d5-9016-e92d922f15b8/OceanDNA-b27620.fa --refList OceanDNA-b27620/target_genomes_gtdb.txt --output OceanDNA-b27620/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:29:36,339] [INFO] Task succeeded: fastANI
[2023-03-18 10:29:36,348] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:29:36,348] [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_900106695.1	s__Albimonas donghaensis	96.9573	975	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	conclusive
GCF_900113695.1	s__Albimonas pacifica	81.5066	731	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	78.2545	409	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_003448965.1	s__Paroceanicella sp003448965	77.9654	421	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887635.2	s__Paroceanicella profunda	77.6584	392	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	77.4264	363	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015679265.1	s__MT2928 sp015679265	77.3804	260	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	77.1965	306	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	77.0728	298	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107585.1	s__Rubrimonas cliftonensis	77.0259	368	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.0156	248	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	76.9756	400	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	76.8727	317	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	76.7593	277	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	76.7069	279	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-18 10:29:36,355] [INFO] GTDB search result was written to OceanDNA-b27620/result_gtdb.tsv
[2023-03-18 10:29:36,369] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:29:36,381] [INFO] DFAST_QC result json was written to OceanDNA-b27620/dqc_result.json
[2023-03-18 10:29:36,381] [INFO] DFAST_QC completed!
[2023-03-18 10:29:36,381] [INFO] Total running time: 0h1m40s