[2024-01-25 19:06:35,578] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:35,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:35,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg75cb32f9-3e8c-4e38-bd8e-f033263d9091/dqc_reference
[2024-01-25 19:06:36,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:36,721] [INFO] Task started: Prodigal
[2024-01-25 19:06:36,722] [INFO] Running command: gunzip -c /var/lib/cwl/stgb04bfb04-d9be-4879-bfb5-712a5e0c95ab/GCF_001005145.1_ASM100514v1_genomic.fna.gz | prodigal -d GCF_001005145.1_ASM100514v1_genomic.fna/cds.fna -a GCF_001005145.1_ASM100514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:54,844] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:54,844] [INFO] Task started: HMMsearch
[2024-01-25 19:06:54,844] [INFO] Running command: hmmsearch --tblout GCF_001005145.1_ASM100514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75cb32f9-3e8c-4e38-bd8e-f033263d9091/dqc_reference/reference_markers.hmm GCF_001005145.1_ASM100514v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:55,205] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:55,206] [INFO] Found 6/6 markers.
[2024-01-25 19:06:55,268] [INFO] Query marker FASTA was written to GCF_001005145.1_ASM100514v1_genomic.fna/markers.fasta
[2024-01-25 19:06:55,268] [INFO] Task started: Blastn
[2024-01-25 19:06:55,269] [INFO] Running command: blastn -query GCF_001005145.1_ASM100514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75cb32f9-3e8c-4e38-bd8e-f033263d9091/dqc_reference/reference_markers.fasta -out GCF_001005145.1_ASM100514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:56,509] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:56,512] [INFO] Selected 15 target genomes.
[2024-01-25 19:06:56,513] [INFO] Target genome list was writen to GCF_001005145.1_ASM100514v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:56,525] [INFO] Task started: fastANI
[2024-01-25 19:06:56,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04bfb04-d9be-4879-bfb5-712a5e0c95ab/GCF_001005145.1_ASM100514v1_genomic.fna.gz --refList GCF_001005145.1_ASM100514v1_genomic.fna/target_genomes.txt --output GCF_001005145.1_ASM100514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:29,365] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:29,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75cb32f9-3e8c-4e38-bd8e-f033263d9091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:29,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75cb32f9-3e8c-4e38-bd8e-f033263d9091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:29,375] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:07:29,376] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:29,376] [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 alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	100.0	2468	2473	95	conclusive
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	99.9934	2472	2473	95	conclusive
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	89.5388	1690	2473	95	below_threshold
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	89.532	1633	2473	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	89.5277	1827	2473	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	89.3711	1793	2473	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	89.3598	1783	2473	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	88.8138	1675	2473	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	87.9847	1769	2473	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	87.9575	1614	2473	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.3809	536	2473	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	76.2996	764	2473	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	76.2568	496	2473	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	76.1278	726	2473	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	75.9952	614	2473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:29,377] [INFO] DFAST Taxonomy check result was written to GCF_001005145.1_ASM100514v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:29,378] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:29,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:29,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75cb32f9-3e8c-4e38-bd8e-f033263d9091/dqc_reference/checkm_data
[2024-01-25 19:07:29,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:29,448] [INFO] Task started: CheckM
[2024-01-25 19:07:29,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001005145.1_ASM100514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001005145.1_ASM100514v1_genomic.fna/checkm_input GCF_001005145.1_ASM100514v1_genomic.fna/checkm_result
[2024-01-25 19:08:58,718] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:58,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:58,749] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:58,749] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:58,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001005145.1_ASM100514v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:58,750] [INFO] Task started: Blastn
[2024-01-25 19:08:58,750] [INFO] Running command: blastn -query GCF_001005145.1_ASM100514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75cb32f9-3e8c-4e38-bd8e-f033263d9091/dqc_reference/reference_markers_gtdb.fasta -out GCF_001005145.1_ASM100514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:00,681] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:00,685] [INFO] Selected 9 target genomes.
[2024-01-25 19:09:00,685] [INFO] Target genome list was writen to GCF_001005145.1_ASM100514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:00,692] [INFO] Task started: fastANI
[2024-01-25 19:09:00,692] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04bfb04-d9be-4879-bfb5-712a5e0c95ab/GCF_001005145.1_ASM100514v1_genomic.fna.gz --refList GCF_001005145.1_ASM100514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001005145.1_ASM100514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:22,903] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:22,910] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:22,910] [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_900105925.1	s__Jiangella alkaliphila	99.9934	2472	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003427025.1	s__Jiangella endophytica	89.5439	1825	2473	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	89.5112	1636	2473	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	89.5062	1694	2473	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	89.3295	1798	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_003579925.1	s__Jiangella rhizosphaerae	89.3061	1525	2473	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	88.841	1671	2473	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	87.972	1770	2473	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	87.9597	1614	2473	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 19:09:22,912] [INFO] GTDB search result was written to GCF_001005145.1_ASM100514v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:22,913] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:22,916] [INFO] DFAST_QC result json was written to GCF_001005145.1_ASM100514v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:22,916] [INFO] DFAST_QC completed!
[2024-01-25 19:09:22,916] [INFO] Total running time: 0h2m47s