[2024-01-25 18:01:50,640] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:01:50,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:01:50,642] [INFO] DQC Reference Directory: /var/lib/cwl/stgd58f5a98-e401-47f8-b271-eee10685a2eb/dqc_reference
[2024-01-25 18:01:51,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:01:51,750] [INFO] Task started: Prodigal
[2024-01-25 18:01:51,750] [INFO] Running command: gunzip -c /var/lib/cwl/stgacab9b2a-c589-4267-8b61-bd613677e66e/GCF_017939745.1_ASM1793974v1_genomic.fna.gz | prodigal -d GCF_017939745.1_ASM1793974v1_genomic.fna/cds.fna -a GCF_017939745.1_ASM1793974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:16,734] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:16,734] [INFO] Task started: HMMsearch
[2024-01-25 18:02:16,734] [INFO] Running command: hmmsearch --tblout GCF_017939745.1_ASM1793974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd58f5a98-e401-47f8-b271-eee10685a2eb/dqc_reference/reference_markers.hmm GCF_017939745.1_ASM1793974v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:17,093] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:17,095] [INFO] Found 6/6 markers.
[2024-01-25 18:02:17,158] [INFO] Query marker FASTA was written to GCF_017939745.1_ASM1793974v1_genomic.fna/markers.fasta
[2024-01-25 18:02:17,158] [INFO] Task started: Blastn
[2024-01-25 18:02:17,159] [INFO] Running command: blastn -query GCF_017939745.1_ASM1793974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd58f5a98-e401-47f8-b271-eee10685a2eb/dqc_reference/reference_markers.fasta -out GCF_017939745.1_ASM1793974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:17,720] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:17,723] [INFO] Selected 16 target genomes.
[2024-01-25 18:02:17,723] [INFO] Target genome list was writen to GCF_017939745.1_ASM1793974v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:17,734] [INFO] Task started: fastANI
[2024-01-25 18:02:17,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgacab9b2a-c589-4267-8b61-bd613677e66e/GCF_017939745.1_ASM1793974v1_genomic.fna.gz --refList GCF_017939745.1_ASM1793974v1_genomic.fna/target_genomes.txt --output GCF_017939745.1_ASM1793974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:37,844] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:37,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd58f5a98-e401-47f8-b271-eee10685a2eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:37,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd58f5a98-e401-47f8-b271-eee10685a2eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:37,855] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:02:37,855] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:02:37,855] [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=UQM 2246	GCA_000171775.1	114	114	type	True	79.9675	1341	3074	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	79.9506	1489	3074	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	79.9462	1500	3074	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	79.9071	1499	3074	95	below_threshold
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	77.5135	824	3074	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	75.0176	50	3074	95	below_threshold
Micromonospora musae	strain=MS1-9	GCA_003626635.1	1894970	1894970	type	True	74.7814	139	3074	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	74.7682	143	3074	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.7509	116	3074	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.7446	130	3074	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	74.7131	166	3074	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	74.6964	122	3074	95	below_threshold
Micromonospora avicenniae	strain=DSM 45758	GCA_900156065.1	1198245	1198245	type	True	74.6464	121	3074	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	74.6181	62	3074	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:37,857] [INFO] DFAST Taxonomy check result was written to GCF_017939745.1_ASM1793974v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:37,857] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:37,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:37,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd58f5a98-e401-47f8-b271-eee10685a2eb/dqc_reference/checkm_data
[2024-01-25 18:02:37,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:37,943] [INFO] Task started: CheckM
[2024-01-25 18:02:37,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017939745.1_ASM1793974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017939745.1_ASM1793974v1_genomic.fna/checkm_input GCF_017939745.1_ASM1793974v1_genomic.fna/checkm_result
[2024-01-25 18:03:44,225] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:44,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:44,254] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:44,254] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:44,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017939745.1_ASM1793974v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:44,255] [INFO] Task started: Blastn
[2024-01-25 18:03:44,255] [INFO] Running command: blastn -query GCF_017939745.1_ASM1793974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd58f5a98-e401-47f8-b271-eee10685a2eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_017939745.1_ASM1793974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:45,069] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:45,072] [INFO] Selected 9 target genomes.
[2024-01-25 18:03:45,072] [INFO] Target genome list was writen to GCF_017939745.1_ASM1793974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:45,100] [INFO] Task started: fastANI
[2024-01-25 18:03:45,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgacab9b2a-c589-4267-8b61-bd613677e66e/GCF_017939745.1_ASM1793974v1_genomic.fna.gz --refList GCF_017939745.1_ASM1793974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017939745.1_ASM1793974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:08,726] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:08,740] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:08,740] [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_017939745.1	s__Gemmata sp017939745	100.0	3074	3074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000531095.1	s__Gemmata massiliana	87.6337	2234	3074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	97.81	97.81	0.89	0.89	2	-
GCF_901538265.1	s__Gemmata massiliana_A	87.4399	2319	3074	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	80.8348	1281	3074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.91	99.90	0.94	0.93	4	-
GCA_017306025.1	s__Gemmata sp017306025	80.0978	1100	3074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013128195.2	s__Gemmata tundricola	80.0315	1528	3074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065095.1	s__Gemmata obscuriglobus	79.9551	1487	3074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.98	99.95	1.00	1.00	4	-
GCA_016872595.1	s__Gemmata sp016872595	79.9336	1155	3074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005773755.1	s__Gemmata sp005773755	79.3776	876	3074	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:08,742] [INFO] GTDB search result was written to GCF_017939745.1_ASM1793974v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:08,743] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:08,746] [INFO] DFAST_QC result json was written to GCF_017939745.1_ASM1793974v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:08,746] [INFO] DFAST_QC completed!
[2024-01-25 18:04:08,746] [INFO] Total running time: 0h2m18s