[2023-03-17 16:13:55,267] [INFO] DFAST_QC pipeline started.
[2023-03-17 16:13:55,268] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 16:13:55,268] [INFO] DQC Reference Directory: /var/lib/cwl/stgc70f8129-e4f4-4e75-9c0f-2d3a7efaeeee/dqc_reference
[2023-03-17 16:13:56,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 16:13:56,402] [INFO] Task started: Prodigal
[2023-03-17 16:13:56,402] [INFO] Running command: cat /var/lib/cwl/stgac4b3756-8889-451f-b25c-09b65b5e1048/OceanDNA-b26884.fa | prodigal -d OceanDNA-b26884/cds.fna -a OceanDNA-b26884/protein.faa -g 11 -q > /dev/null
[2023-03-17 16:14:16,120] [INFO] Task succeeded: Prodigal
[2023-03-17 16:14:16,120] [INFO] Task started: HMMsearch
[2023-03-17 16:14:16,120] [INFO] Running command: hmmsearch --tblout OceanDNA-b26884/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc70f8129-e4f4-4e75-9c0f-2d3a7efaeeee/dqc_reference/reference_markers.hmm OceanDNA-b26884/protein.faa > /dev/null
[2023-03-17 16:14:16,383] [INFO] Task succeeded: HMMsearch
[2023-03-17 16:14:16,383] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgac4b3756-8889-451f-b25c-09b65b5e1048/OceanDNA-b26884.fa]
[2023-03-17 16:14:16,409] [INFO] Query marker FASTA was written to OceanDNA-b26884/markers.fasta
[2023-03-17 16:14:16,409] [INFO] Task started: Blastn
[2023-03-17 16:14:16,409] [INFO] Running command: blastn -query OceanDNA-b26884/markers.fasta -db /var/lib/cwl/stgc70f8129-e4f4-4e75-9c0f-2d3a7efaeeee/dqc_reference/reference_markers.fasta -out OceanDNA-b26884/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:14:17,133] [INFO] Task succeeded: Blastn
[2023-03-17 16:14:17,134] [INFO] Selected 14 target genomes.
[2023-03-17 16:14:17,134] [INFO] Target genome list was writen to OceanDNA-b26884/target_genomes.txt
[2023-03-17 16:14:17,143] [INFO] Task started: fastANI
[2023-03-17 16:14:17,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgac4b3756-8889-451f-b25c-09b65b5e1048/OceanDNA-b26884.fa --refList OceanDNA-b26884/target_genomes.txt --output OceanDNA-b26884/fastani_result.tsv --threads 1
[2023-03-17 16:14:36,348] [INFO] Task succeeded: fastANI
[2023-03-17 16:14:36,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc70f8129-e4f4-4e75-9c0f-2d3a7efaeeee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 16:14:36,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc70f8129-e4f4-4e75-9c0f-2d3a7efaeeee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 16:14:36,357] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 16:14:36,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 16:14:36,357] [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
Martelella lutilitoris	strain=GH2-6	GCA_005924265.1	2583532	2583532	type	True	90.0436	911	1093	95	below_threshold
Martelella radicis	strain=DSM 28101	GCA_014196625.1	1397476	1397476	type	True	88.6391	881	1093	95	below_threshold
Martelella mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	82.5157	710	1093	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	82.4901	694	1093	95	below_threshold
Martelella endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	81.9122	656	1093	95	below_threshold
Martelella limonii	strain=NBRC 109441	GCA_013344475.1	1647649	1647649	type	True	81.1085	642	1093	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.2606	351	1093	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.9815	384	1093	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.7606	266	1093	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.662	325	1093	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	77.5601	332	1093	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	77.4788	314	1093	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	77.0442	226	1093	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	76.1826	108	1093	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 16:14:36,357] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26884/tc_result.tsv
[2023-03-17 16:14:36,357] [INFO] ===== Taxonomy check completed =====
[2023-03-17 16:14:36,357] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 16:14:36,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc70f8129-e4f4-4e75-9c0f-2d3a7efaeeee/dqc_reference/checkm_data
[2023-03-17 16:14:36,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 16:14:36,364] [INFO] Task started: CheckM
[2023-03-17 16:14:36,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26884/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26884/checkm_input OceanDNA-b26884/checkm_result
[2023-03-17 16:15:40,075] [INFO] Task succeeded: CheckM
[2023-03-17 16:15:40,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 16:15:40,078] [INFO] ===== Completeness check finished =====
[2023-03-17 16:15:40,078] [INFO] ===== Start GTDB Search =====
[2023-03-17 16:15:40,078] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26884/markers.fasta)
[2023-03-17 16:15:40,079] [INFO] Task started: Blastn
[2023-03-17 16:15:40,080] [INFO] Running command: blastn -query OceanDNA-b26884/markers.fasta -db /var/lib/cwl/stgc70f8129-e4f4-4e75-9c0f-2d3a7efaeeee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26884/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:15:41,340] [INFO] Task succeeded: Blastn
[2023-03-17 16:15:41,340] [INFO] Selected 7 target genomes.
[2023-03-17 16:15:41,340] [INFO] Target genome list was writen to OceanDNA-b26884/target_genomes_gtdb.txt
[2023-03-17 16:15:41,419] [INFO] Task started: fastANI
[2023-03-17 16:15:41,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgac4b3756-8889-451f-b25c-09b65b5e1048/OceanDNA-b26884.fa --refList OceanDNA-b26884/target_genomes_gtdb.txt --output OceanDNA-b26884/fastani_result_gtdb.tsv --threads 1
[2023-03-17 16:15:49,271] [INFO] Task succeeded: fastANI
[2023-03-17 16:15:49,276] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 16:15:49,276] [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_001578105.1	s__Martelella sp001578105	98.7023	1072	1093	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.55	95.11	0.93	0.87	3	conclusive
GCF_005924265.1	s__Martelella lutilitoris	90.0478	911	1093	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196625.1	s__Martelella radicis	88.6325	881	1093	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001975.1	s__Martelella mediterranea_A	84.0117	717	1093	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043005.1	s__Martelella mediterranea	82.4954	714	1093	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.32	95.96	0.90	0.83	4	-
GCF_013459645.1	s__Martelella sp013459645	81.9333	701	1093	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000960975.1	s__Martelella endophytica	81.8181	665	1093	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 16:15:49,276] [INFO] GTDB search result was written to OceanDNA-b26884/result_gtdb.tsv
[2023-03-17 16:15:49,276] [INFO] ===== GTDB Search completed =====
[2023-03-17 16:15:49,277] [INFO] DFAST_QC result json was written to OceanDNA-b26884/dqc_result.json
[2023-03-17 16:15:49,278] [INFO] DFAST_QC completed!
[2023-03-17 16:15:49,278] [INFO] Total running time: 0h1m54s