[2024-01-25 19:49:05,639] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:05,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:05,641] [INFO] DQC Reference Directory: /var/lib/cwl/stgd767858e-7b60-47b5-8667-d18440e880b7/dqc_reference
[2024-01-25 19:49:06,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:06,791] [INFO] Task started: Prodigal
[2024-01-25 19:49:06,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg9581ac8d-b2b3-4f42-b189-52e543ad1fe8/GCF_003014555.1_ASM301455v1_genomic.fna.gz | prodigal -d GCF_003014555.1_ASM301455v1_genomic.fna/cds.fna -a GCF_003014555.1_ASM301455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:21,133] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:21,133] [INFO] Task started: HMMsearch
[2024-01-25 19:49:21,133] [INFO] Running command: hmmsearch --tblout GCF_003014555.1_ASM301455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd767858e-7b60-47b5-8667-d18440e880b7/dqc_reference/reference_markers.hmm GCF_003014555.1_ASM301455v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:21,502] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:21,503] [INFO] Found 6/6 markers.
[2024-01-25 19:49:21,548] [INFO] Query marker FASTA was written to GCF_003014555.1_ASM301455v1_genomic.fna/markers.fasta
[2024-01-25 19:49:21,548] [INFO] Task started: Blastn
[2024-01-25 19:49:21,548] [INFO] Running command: blastn -query GCF_003014555.1_ASM301455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd767858e-7b60-47b5-8667-d18440e880b7/dqc_reference/reference_markers.fasta -out GCF_003014555.1_ASM301455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:22,658] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:22,661] [INFO] Selected 15 target genomes.
[2024-01-25 19:49:22,661] [INFO] Target genome list was writen to GCF_003014555.1_ASM301455v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:22,691] [INFO] Task started: fastANI
[2024-01-25 19:49:22,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg9581ac8d-b2b3-4f42-b189-52e543ad1fe8/GCF_003014555.1_ASM301455v1_genomic.fna.gz --refList GCF_003014555.1_ASM301455v1_genomic.fna/target_genomes.txt --output GCF_003014555.1_ASM301455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:42,294] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:42,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd767858e-7b60-47b5-8667-d18440e880b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:42,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd767858e-7b60-47b5-8667-d18440e880b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:42,307] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:49:42,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:42,307] [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
Haloactinopolyspora alba	strain=DSM 45211	GCA_003014555.1	648780	648780	type	True	100.0	1817	1822	95	conclusive
Haloactinopolyspora alba	strain=YIM 93246	GCA_004138525.1	648780	648780	type	True	99.9954	1808	1822	95	conclusive
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	80.6406	918	1822	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	80.4181	901	1822	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	80.28	1017	1822	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	80.2755	1015	1822	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	80.2599	968	1822	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	80.1863	963	1822	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	80.1499	990	1822	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	80.1493	992	1822	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.4551	268	1822	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	76.4099	409	1822	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	76.2543	603	1822	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.1076	375	1822	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	76.0961	420	1822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:42,308] [INFO] DFAST Taxonomy check result was written to GCF_003014555.1_ASM301455v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:42,309] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:42,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:42,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd767858e-7b60-47b5-8667-d18440e880b7/dqc_reference/checkm_data
[2024-01-25 19:49:42,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:42,361] [INFO] Task started: CheckM
[2024-01-25 19:49:42,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014555.1_ASM301455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014555.1_ASM301455v1_genomic.fna/checkm_input GCF_003014555.1_ASM301455v1_genomic.fna/checkm_result
[2024-01-25 19:50:47,492] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:47,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:47,517] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:47,517] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:47,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014555.1_ASM301455v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:47,518] [INFO] Task started: Blastn
[2024-01-25 19:50:47,518] [INFO] Running command: blastn -query GCF_003014555.1_ASM301455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd767858e-7b60-47b5-8667-d18440e880b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014555.1_ASM301455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:49,252] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:49,255] [INFO] Selected 11 target genomes.
[2024-01-25 19:50:49,255] [INFO] Target genome list was writen to GCF_003014555.1_ASM301455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:49,262] [INFO] Task started: fastANI
[2024-01-25 19:50:49,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg9581ac8d-b2b3-4f42-b189-52e543ad1fe8/GCF_003014555.1_ASM301455v1_genomic.fna.gz --refList GCF_003014555.1_ASM301455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014555.1_ASM301455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:05,353] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:05,361] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:05,362] [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_003014555.1	s__Haloactinopolyspora alba	100.0	1817	1822	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Haloactinopolyspora	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003579925.1	s__Jiangella rhizosphaerae	80.5828	928	1822	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515395.1	s__Jiangella gansuensis	80.3843	907	1822	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	80.3292	985	1822	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004349105.1	s__Jiangella aurantiaca	80.3271	964	1822	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349065.1	s__Jiangella asiatica	80.3072	938	1822	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	80.2876	963	1822	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	80.2742	1016	1822	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_014204975.1	s__Jiangella mangrovi	80.2077	959	1822	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	80.1648	987	1822	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003427025.1	s__Jiangella endophytica	80.1527	992	1822	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 19:51:05,363] [INFO] GTDB search result was written to GCF_003014555.1_ASM301455v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:05,363] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:05,367] [INFO] DFAST_QC result json was written to GCF_003014555.1_ASM301455v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:05,367] [INFO] DFAST_QC completed!
[2024-01-25 19:51:05,367] [INFO] Total running time: 0h1m60s