[2024-01-24 13:27:31,550] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0ba7fa4-3f01-424b-bc24-36259ca63464/dqc_reference
[2024-01-24 13:27:32,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:32,899] [INFO] Task started: Prodigal
[2024-01-24 13:27:32,900] [INFO] Running command: gunzip -c /var/lib/cwl/stg9db2e843-4f51-4f97-b435-92c6e8ea499b/GCF_008065095.1_ASM806509v1_genomic.fna.gz | prodigal -d GCF_008065095.1_ASM806509v1_genomic.fna/cds.fna -a GCF_008065095.1_ASM806509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:01,193] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:01,194] [INFO] Task started: HMMsearch
[2024-01-24 13:28:01,194] [INFO] Running command: hmmsearch --tblout GCF_008065095.1_ASM806509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0ba7fa4-3f01-424b-bc24-36259ca63464/dqc_reference/reference_markers.hmm GCF_008065095.1_ASM806509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:01,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:01,581] [INFO] Found 6/6 markers.
[2024-01-24 13:28:01,652] [INFO] Query marker FASTA was written to GCF_008065095.1_ASM806509v1_genomic.fna/markers.fasta
[2024-01-24 13:28:01,652] [INFO] Task started: Blastn
[2024-01-24 13:28:01,652] [INFO] Running command: blastn -query GCF_008065095.1_ASM806509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0ba7fa4-3f01-424b-bc24-36259ca63464/dqc_reference/reference_markers.fasta -out GCF_008065095.1_ASM806509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:02,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:02,347] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:02,347] [INFO] Target genome list was writen to GCF_008065095.1_ASM806509v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:02,369] [INFO] Task started: fastANI
[2024-01-24 13:28:02,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg9db2e843-4f51-4f97-b435-92c6e8ea499b/GCF_008065095.1_ASM806509v1_genomic.fna.gz --refList GCF_008065095.1_ASM806509v1_genomic.fna/target_genomes.txt --output GCF_008065095.1_ASM806509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:30,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:30,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0ba7fa4-3f01-424b-bc24-36259ca63464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:30,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0ba7fa4-3f01-424b-bc24-36259ca63464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:30,428] [INFO] Found 14 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:28:30,428] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:30,428] [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
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	100.0	2999	2999	95	conclusive
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	99.9982	2997	2999	95	conclusive
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	99.998	2998	2999	95	conclusive
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	99.8005	2605	2999	95	conclusive
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	78.0813	957	2999	95	below_threshold
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	76.6692	618	2999	95	below_threshold
Dietzia timorensis	strain=ID05-A0528	GCA_001659785.1	499555	499555	type	True	74.9325	52	2999	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.9063	166	2999	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.9062	191	2999	95	below_threshold
Brachybacterium muris	strain=DSM 15460	GCA_016907455.1	219301	219301	type	True	74.817	66	2999	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	74.8132	98	2999	95	below_threshold
Phytoactinopolyspora halophila	strain=YIM 96934	GCA_003287285.1	1981511	1981511	type	True	74.7569	79	2999	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	74.7251	118	2999	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	74.6693	176	2999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:30,429] [INFO] DFAST Taxonomy check result was written to GCF_008065095.1_ASM806509v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:30,430] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:30,430] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:30,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0ba7fa4-3f01-424b-bc24-36259ca63464/dqc_reference/checkm_data
[2024-01-24 13:28:30,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:30,510] [INFO] Task started: CheckM
[2024-01-24 13:28:30,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008065095.1_ASM806509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008065095.1_ASM806509v1_genomic.fna/checkm_input GCF_008065095.1_ASM806509v1_genomic.fna/checkm_result
[2024-01-24 13:29:47,646] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:47,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:47,678] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:47,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:47,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008065095.1_ASM806509v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:47,679] [INFO] Task started: Blastn
[2024-01-24 13:29:47,679] [INFO] Running command: blastn -query GCF_008065095.1_ASM806509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0ba7fa4-3f01-424b-bc24-36259ca63464/dqc_reference/reference_markers_gtdb.fasta -out GCF_008065095.1_ASM806509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:48,609] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:48,614] [INFO] Selected 11 target genomes.
[2024-01-24 13:29:48,614] [INFO] Target genome list was writen to GCF_008065095.1_ASM806509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:48,625] [INFO] Task started: fastANI
[2024-01-24 13:29:48,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg9db2e843-4f51-4f97-b435-92c6e8ea499b/GCF_008065095.1_ASM806509v1_genomic.fna.gz --refList GCF_008065095.1_ASM806509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008065095.1_ASM806509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:13,458] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:13,470] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:13,470] [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_008065095.1	s__Gemmata obscuriglobus	100.0	2999	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.98	99.95	1.00	1.00	4	conclusive
GCF_017939745.1	s__Gemmata sp017939745	80.0319	1487	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306025.1	s__Gemmata sp017306025	79.9314	1025	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000531095.1	s__Gemmata massiliana	79.7939	1417	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	97.81	97.81	0.89	0.89	2	-
GCF_013128195.2	s__Gemmata tundricola	79.787	1368	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901538265.1	s__Gemmata massiliana_A	79.7603	1418	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872595.1	s__Gemmata sp016872595	79.5668	1067	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901538445.1	s__Gemmata sp901538445	79.1496	1120	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005772955.1	s__Gemmata sp005772955	78.9292	986	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.91	99.90	0.94	0.93	4	-
GCA_005773755.1	s__Gemmata sp005773755	78.8891	765	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	78.0246	971	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:13,473] [INFO] GTDB search result was written to GCF_008065095.1_ASM806509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:13,474] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:13,488] [INFO] DFAST_QC result json was written to GCF_008065095.1_ASM806509v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:13,488] [INFO] DFAST_QC completed!
[2024-01-24 13:30:13,488] [INFO] Total running time: 0h2m42s