[2024-01-25 18:13:50,928] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:50,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:50,933] [INFO] DQC Reference Directory: /var/lib/cwl/stgeee5489c-2210-44b6-b1c6-0fd886c910ac/dqc_reference
[2024-01-25 18:13:52,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:52,118] [INFO] Task started: Prodigal
[2024-01-25 18:13:52,119] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9da3ff7-8c7e-42f3-9609-76d9f1d33d6d/GCF_028368995.1_ASM2836899v1_genomic.fna.gz | prodigal -d GCF_028368995.1_ASM2836899v1_genomic.fna/cds.fna -a GCF_028368995.1_ASM2836899v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:18,878] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:18,879] [INFO] Task started: HMMsearch
[2024-01-25 18:14:18,879] [INFO] Running command: hmmsearch --tblout GCF_028368995.1_ASM2836899v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeee5489c-2210-44b6-b1c6-0fd886c910ac/dqc_reference/reference_markers.hmm GCF_028368995.1_ASM2836899v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:19,357] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:19,358] [INFO] Found 6/6 markers.
[2024-01-25 18:14:19,436] [INFO] Query marker FASTA was written to GCF_028368995.1_ASM2836899v1_genomic.fna/markers.fasta
[2024-01-25 18:14:19,436] [INFO] Task started: Blastn
[2024-01-25 18:14:19,436] [INFO] Running command: blastn -query GCF_028368995.1_ASM2836899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeee5489c-2210-44b6-b1c6-0fd886c910ac/dqc_reference/reference_markers.fasta -out GCF_028368995.1_ASM2836899v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:20,233] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:20,239] [INFO] Selected 27 target genomes.
[2024-01-25 18:14:20,239] [INFO] Target genome list was writen to GCF_028368995.1_ASM2836899v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:20,268] [INFO] Task started: fastANI
[2024-01-25 18:14:20,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9da3ff7-8c7e-42f3-9609-76d9f1d33d6d/GCF_028368995.1_ASM2836899v1_genomic.fna.gz --refList GCF_028368995.1_ASM2836899v1_genomic.fna/target_genomes.txt --output GCF_028368995.1_ASM2836899v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:55,193] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:55,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeee5489c-2210-44b6-b1c6-0fd886c910ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:55,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeee5489c-2210-44b6-b1c6-0fd886c910ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:55,208] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:14:55,208] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:14:55,208] [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
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	89.879	2999	3681	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	89.8736	2930	3681	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	76.1312	1118	3681	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.3868	286	3681	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	75.2979	88	3681	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	75.2978	89	3681	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	75.2919	82	3681	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.1639	486	3681	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.1237	912	3681	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	75.1108	476	3681	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.0714	646	3681	95	below_threshold
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	75.07	219	3681	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.0376	410	3681	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	74.9917	178	3681	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	74.99	375	3681	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	74.982	158	3681	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	74.9629	286	3681	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	74.9501	500	3681	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	74.912	180	3681	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	74.9089	402	3681	95	below_threshold
Acuticoccus sediminis	strain=PTG4-2	GCA_003258595.1	2184697	2184697	type	True	74.8949	546	3681	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	74.8927	266	3681	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	74.8723	277	3681	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	74.8089	212	3681	95	below_threshold
Bifidobacterium rousetti	strain=RST9	GCA_008698235.1	2045439	2045439	type	True	74.8082	162	3681	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	74.8022	601	3681	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	74.7741	689	3681	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:55,210] [INFO] DFAST Taxonomy check result was written to GCF_028368995.1_ASM2836899v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:55,210] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:55,210] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:55,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeee5489c-2210-44b6-b1c6-0fd886c910ac/dqc_reference/checkm_data
[2024-01-25 18:14:55,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:55,311] [INFO] Task started: CheckM
[2024-01-25 18:14:55,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028368995.1_ASM2836899v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028368995.1_ASM2836899v1_genomic.fna/checkm_input GCF_028368995.1_ASM2836899v1_genomic.fna/checkm_result
[2024-01-25 18:17:02,485] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:02,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:02,512] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:02,513] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:02,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028368995.1_ASM2836899v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:02,514] [INFO] Task started: Blastn
[2024-01-25 18:17:02,514] [INFO] Running command: blastn -query GCF_028368995.1_ASM2836899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeee5489c-2210-44b6-b1c6-0fd886c910ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_028368995.1_ASM2836899v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:03,868] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:03,871] [INFO] Selected 9 target genomes.
[2024-01-25 18:17:03,871] [INFO] Target genome list was writen to GCF_028368995.1_ASM2836899v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:03,877] [INFO] Task started: fastANI
[2024-01-25 18:17:03,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9da3ff7-8c7e-42f3-9609-76d9f1d33d6d/GCF_028368995.1_ASM2836899v1_genomic.fna.gz --refList GCF_028368995.1_ASM2836899v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028368995.1_ASM2836899v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:28,703] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:28,710] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:17:28,710] [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_002343915.1	s__Nannocystis exedens	89.8525	3004	3681	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013812955.1	s__Nannocystis sp013812955	79.9468	1135	3681	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793465.1	s__Nannocystis sp016793465	79.4968	1924	3681	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714285.1	s__Nannocystis sp016714285	79.4817	1646	3681	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCA_016712315.1	s__JADJRG01 sp016712315	76.8752	1121	3681	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	76.3215	1111	3681	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCF_000170895.1	s__Plesiocystis pacifica	76.1053	1124	3681	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464385.1	s__Ga0077550 sp001464385	76.1008	1265	3681	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001915025.1	s__20CM-2-65-7 sp001915025	74.7015	94	3681	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-2-65-7	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:28,712] [INFO] GTDB search result was written to GCF_028368995.1_ASM2836899v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:28,712] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:28,715] [INFO] DFAST_QC result json was written to GCF_028368995.1_ASM2836899v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:28,716] [INFO] DFAST_QC completed!
[2024-01-25 18:17:28,716] [INFO] Total running time: 0h3m38s