[2024-01-24 13:40:33,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,367] [INFO] DQC Reference Directory: /var/lib/cwl/stga7d2cf0d-0e97-492b-8516-104f12902113/dqc_reference
[2024-01-24 13:40:34,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,772] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,772] [INFO] Running command: gunzip -c /var/lib/cwl/stgd690560e-d570-4d67-9a10-05592b616e83/GCF_003579925.1_ASM357992v1_genomic.fna.gz | prodigal -d GCF_003579925.1_ASM357992v1_genomic.fna/cds.fna -a GCF_003579925.1_ASM357992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:50,693] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:50,693] [INFO] Task started: HMMsearch
[2024-01-24 13:40:50,693] [INFO] Running command: hmmsearch --tblout GCF_003579925.1_ASM357992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7d2cf0d-0e97-492b-8516-104f12902113/dqc_reference/reference_markers.hmm GCF_003579925.1_ASM357992v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:51,045] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:51,046] [INFO] Found 6/6 markers.
[2024-01-24 13:40:51,101] [INFO] Query marker FASTA was written to GCF_003579925.1_ASM357992v1_genomic.fna/markers.fasta
[2024-01-24 13:40:51,102] [INFO] Task started: Blastn
[2024-01-24 13:40:51,102] [INFO] Running command: blastn -query GCF_003579925.1_ASM357992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d2cf0d-0e97-492b-8516-104f12902113/dqc_reference/reference_markers.fasta -out GCF_003579925.1_ASM357992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:52,459] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:52,462] [INFO] Selected 15 target genomes.
[2024-01-24 13:40:52,462] [INFO] Target genome list was writen to GCF_003579925.1_ASM357992v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:52,471] [INFO] Task started: fastANI
[2024-01-24 13:40:52,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgd690560e-d570-4d67-9a10-05592b616e83/GCF_003579925.1_ASM357992v1_genomic.fna.gz --refList GCF_003579925.1_ASM357992v1_genomic.fna/target_genomes.txt --output GCF_003579925.1_ASM357992v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:28,319] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:28,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7d2cf0d-0e97-492b-8516-104f12902113/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:28,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7d2cf0d-0e97-492b-8516-104f12902113/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:28,333] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:28,333] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:28,334] [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
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	100.0	1942	1956	95	conclusive
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	91.3117	1479	1956	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	89.5021	1506	1956	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	89.4893	1546	1956	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	89.2522	1581	1956	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	89.0047	1553	1956	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	88.9904	1554	1956	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	88.915	1464	1956	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	88.5778	1453	1956	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	87.9947	1555	1956	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	76.4444	724	1956	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	76.4288	569	1956	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	76.3889	646	1956	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	76.2956	681	1956	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	76.2044	632	1956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:28,335] [INFO] DFAST Taxonomy check result was written to GCF_003579925.1_ASM357992v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:28,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:28,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:28,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7d2cf0d-0e97-492b-8516-104f12902113/dqc_reference/checkm_data
[2024-01-24 13:41:28,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:28,407] [INFO] Task started: CheckM
[2024-01-24 13:41:28,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003579925.1_ASM357992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003579925.1_ASM357992v1_genomic.fna/checkm_input GCF_003579925.1_ASM357992v1_genomic.fna/checkm_result
[2024-01-24 13:42:42,599] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:42,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:42,625] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:42,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:42,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003579925.1_ASM357992v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:42,626] [INFO] Task started: Blastn
[2024-01-24 13:42:42,626] [INFO] Running command: blastn -query GCF_003579925.1_ASM357992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d2cf0d-0e97-492b-8516-104f12902113/dqc_reference/reference_markers_gtdb.fasta -out GCF_003579925.1_ASM357992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:44,664] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:44,668] [INFO] Selected 9 target genomes.
[2024-01-24 13:42:44,668] [INFO] Target genome list was writen to GCF_003579925.1_ASM357992v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:44,695] [INFO] Task started: fastANI
[2024-01-24 13:42:44,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgd690560e-d570-4d67-9a10-05592b616e83/GCF_003579925.1_ASM357992v1_genomic.fna.gz --refList GCF_003579925.1_ASM357992v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003579925.1_ASM357992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:08,781] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:08,793] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:08,793] [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_003579925.1	s__Jiangella rhizosphaerae	100.0	1942	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004349105.1	s__Jiangella aurantiaca	91.3077	1479	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105925.1	s__Jiangella alkaliphila	89.4949	1544	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003427025.1	s__Jiangella endophytica	89.2432	1582	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270745.1	s__Jiangella muralis	88.9594	1458	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106035.1	s__Jiangella alba	88.9526	1559	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_003236295.1	s__Jiangella anatolica	88.6001	1451	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348545.1	s__Jiangella ureilytica	88.2157	1431	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204975.1	s__Jiangella mangrovi	88.0194	1552	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:08,795] [INFO] GTDB search result was written to GCF_003579925.1_ASM357992v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:08,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:08,799] [INFO] DFAST_QC result json was written to GCF_003579925.1_ASM357992v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:08,799] [INFO] DFAST_QC completed!
[2024-01-24 13:43:08,799] [INFO] Total running time: 0h2m35s