[2024-01-25 19:47:05,559] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:05,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:05,565] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe96bd8e-6699-498c-9115-29f856e57fca/dqc_reference
[2024-01-25 19:47:06,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:06,675] [INFO] Task started: Prodigal
[2024-01-25 19:47:06,675] [INFO] Running command: gunzip -c /var/lib/cwl/stga721586c-858f-4fff-bf47-67db02c837b6/GCF_014204975.1_ASM1420497v1_genomic.fna.gz | prodigal -d GCF_014204975.1_ASM1420497v1_genomic.fna/cds.fna -a GCF_014204975.1_ASM1420497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:23,977] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:23,978] [INFO] Task started: HMMsearch
[2024-01-25 19:47:23,978] [INFO] Running command: hmmsearch --tblout GCF_014204975.1_ASM1420497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe96bd8e-6699-498c-9115-29f856e57fca/dqc_reference/reference_markers.hmm GCF_014204975.1_ASM1420497v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:24,264] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:24,265] [INFO] Found 6/6 markers.
[2024-01-25 19:47:24,320] [INFO] Query marker FASTA was written to GCF_014204975.1_ASM1420497v1_genomic.fna/markers.fasta
[2024-01-25 19:47:24,320] [INFO] Task started: Blastn
[2024-01-25 19:47:24,320] [INFO] Running command: blastn -query GCF_014204975.1_ASM1420497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe96bd8e-6699-498c-9115-29f856e57fca/dqc_reference/reference_markers.fasta -out GCF_014204975.1_ASM1420497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:25,626] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:25,631] [INFO] Selected 16 target genomes.
[2024-01-25 19:47:25,631] [INFO] Target genome list was writen to GCF_014204975.1_ASM1420497v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:25,637] [INFO] Task started: fastANI
[2024-01-25 19:47:25,637] [INFO] Running command: fastANI --query /var/lib/cwl/stga721586c-858f-4fff-bf47-67db02c837b6/GCF_014204975.1_ASM1420497v1_genomic.fna.gz --refList GCF_014204975.1_ASM1420497v1_genomic.fna/target_genomes.txt --output GCF_014204975.1_ASM1420497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:01,145] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:01,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe96bd8e-6699-498c-9115-29f856e57fca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:01,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe96bd8e-6699-498c-9115-29f856e57fca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:01,157] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:48:01,157] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:01,157] [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 mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	100.0	2386	2388	95	conclusive
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	91.0847	1740	2388	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	87.9765	1756	2388	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	87.9543	1532	2388	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	87.8627	1810	2388	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	87.6621	1750	2388	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	87.6492	1742	2388	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	87.6454	1775	2388	95	below_threshold
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	87.6136	1583	2388	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	87.4528	1657	2388	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	87.2714	1606	2388	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	76.3082	749	2388	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	76.2897	723	2388	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	76.255	867	2388	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	76.2089	759	2388	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	76.1377	963	2388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:01,159] [INFO] DFAST Taxonomy check result was written to GCF_014204975.1_ASM1420497v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:01,159] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:01,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:01,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe96bd8e-6699-498c-9115-29f856e57fca/dqc_reference/checkm_data
[2024-01-25 19:48:01,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:01,224] [INFO] Task started: CheckM
[2024-01-25 19:48:01,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014204975.1_ASM1420497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014204975.1_ASM1420497v1_genomic.fna/checkm_input GCF_014204975.1_ASM1420497v1_genomic.fna/checkm_result
[2024-01-25 19:50:19,385] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:19,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:19,408] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:19,408] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:19,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014204975.1_ASM1420497v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:19,411] [INFO] Task started: Blastn
[2024-01-25 19:50:19,411] [INFO] Running command: blastn -query GCF_014204975.1_ASM1420497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe96bd8e-6699-498c-9115-29f856e57fca/dqc_reference/reference_markers_gtdb.fasta -out GCF_014204975.1_ASM1420497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:21,544] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:21,547] [INFO] Selected 9 target genomes.
[2024-01-25 19:50:21,547] [INFO] Target genome list was writen to GCF_014204975.1_ASM1420497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:21,557] [INFO] Task started: fastANI
[2024-01-25 19:50:21,557] [INFO] Running command: fastANI --query /var/lib/cwl/stga721586c-858f-4fff-bf47-67db02c837b6/GCF_014204975.1_ASM1420497v1_genomic.fna.gz --refList GCF_014204975.1_ASM1420497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014204975.1_ASM1420497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:43,215] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:43,222] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:43,222] [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_014204975.1	s__Jiangella mangrovi	100.0	2386	2388	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_004348545.1	s__Jiangella ureilytica	91.0667	1742	2388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003579925.1	s__Jiangella rhizosphaerae	88.0016	1527	2388	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	87.9418	1799	2388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900106035.1	s__Jiangella alba	87.6566	1753	2388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_003427025.1	s__Jiangella endophytica	87.6389	1776	2388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349105.1	s__Jiangella aurantiaca	87.5562	1589	2388	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	87.4432	1658	2388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236295.1	s__Jiangella anatolica	87.3351	1597	2388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:43,223] [INFO] GTDB search result was written to GCF_014204975.1_ASM1420497v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:43,224] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:43,227] [INFO] DFAST_QC result json was written to GCF_014204975.1_ASM1420497v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:43,227] [INFO] DFAST_QC completed!
[2024-01-25 19:50:43,227] [INFO] Total running time: 0h3m38s