[2024-01-24 14:39:15,641] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,650] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg29f01064-3d8c-4cb9-a81e-2ec9c6fbc4ba/dqc_reference
[2024-01-24 14:39:18,587] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:18,588] [INFO] Task started: Prodigal
[2024-01-24 14:39:18,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg19699770-ba7a-4a48-ab2f-04309dd65cb4/GCF_004919045.1_ASM491904v1_genomic.fna.gz | prodigal -d GCF_004919045.1_ASM491904v1_genomic.fna/cds.fna -a GCF_004919045.1_ASM491904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:30,008] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:30,008] [INFO] Task started: HMMsearch
[2024-01-24 14:39:30,009] [INFO] Running command: hmmsearch --tblout GCF_004919045.1_ASM491904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29f01064-3d8c-4cb9-a81e-2ec9c6fbc4ba/dqc_reference/reference_markers.hmm GCF_004919045.1_ASM491904v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:30,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:30,287] [INFO] Found 6/6 markers.
[2024-01-24 14:39:30,324] [INFO] Query marker FASTA was written to GCF_004919045.1_ASM491904v1_genomic.fna/markers.fasta
[2024-01-24 14:39:30,325] [INFO] Task started: Blastn
[2024-01-24 14:39:30,325] [INFO] Running command: blastn -query GCF_004919045.1_ASM491904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29f01064-3d8c-4cb9-a81e-2ec9c6fbc4ba/dqc_reference/reference_markers.fasta -out GCF_004919045.1_ASM491904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:31,605] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:31,610] [INFO] Selected 12 target genomes.
[2024-01-24 14:39:31,611] [INFO] Target genome list was writen to GCF_004919045.1_ASM491904v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:31,632] [INFO] Task started: fastANI
[2024-01-24 14:39:31,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg19699770-ba7a-4a48-ab2f-04309dd65cb4/GCF_004919045.1_ASM491904v1_genomic.fna.gz --refList GCF_004919045.1_ASM491904v1_genomic.fna/target_genomes.txt --output GCF_004919045.1_ASM491904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:41,562] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:41,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29f01064-3d8c-4cb9-a81e-2ec9c6fbc4ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:41,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29f01064-3d8c-4cb9-a81e-2ec9c6fbc4ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:41,573] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:41,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:41,574] [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
Sinomonas albida	strain=LC13	GCA_004919045.1	369942	369942	type	True	100.0	1240	1241	95	conclusive
Sinomonas susongensis	strain=A31	GCA_005877005.1	1324851	1324851	type	True	82.2834	763	1241	95	below_threshold
Sinomonas humi	strain=MUSC 117	GCA_000802235.1	1338436	1338436	type	True	81.8845	748	1241	95	below_threshold
Sinomonas atrocyanea	strain=CGMCC 1.1891	GCA_014644475.1	37927	37927	type	True	81.5221	708	1241	95	below_threshold
Sinomonas atrocyanea	strain=KCTC 3377	GCA_001577305.1	37927	37927	type	True	81.4888	750	1241	95	below_threshold
Sinomonas atrocyanea	strain=NBRC 12956	GCA_006539205.1	37927	37927	type	True	81.485	728	1241	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	81.4787	697	1241	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	80.2814	610	1241	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.9366	277	1241	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.7972	178	1241	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.4187	226	1241	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.3832	228	1241	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:41,577] [INFO] DFAST Taxonomy check result was written to GCF_004919045.1_ASM491904v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:41,578] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:41,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:41,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29f01064-3d8c-4cb9-a81e-2ec9c6fbc4ba/dqc_reference/checkm_data
[2024-01-24 14:39:41,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:41,616] [INFO] Task started: CheckM
[2024-01-24 14:39:41,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004919045.1_ASM491904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004919045.1_ASM491904v1_genomic.fna/checkm_input GCF_004919045.1_ASM491904v1_genomic.fna/checkm_result
[2024-01-24 14:40:18,484] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:18,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:18,564] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:18,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:18,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004919045.1_ASM491904v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:18,566] [INFO] Task started: Blastn
[2024-01-24 14:40:18,566] [INFO] Running command: blastn -query GCF_004919045.1_ASM491904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29f01064-3d8c-4cb9-a81e-2ec9c6fbc4ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_004919045.1_ASM491904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:20,663] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:20,667] [INFO] Selected 8 target genomes.
[2024-01-24 14:40:20,668] [INFO] Target genome list was writen to GCF_004919045.1_ASM491904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:20,675] [INFO] Task started: fastANI
[2024-01-24 14:40:20,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg19699770-ba7a-4a48-ab2f-04309dd65cb4/GCF_004919045.1_ASM491904v1_genomic.fna.gz --refList GCF_004919045.1_ASM491904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004919045.1_ASM491904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:29,297] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:29,309] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:29,309] [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_004919045.1	s__Sinomonas albida	100.0	1240	1241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005877005.1	s__Sinomonas susongensis	82.2906	762	1241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005876955.1	s__Sinomonas sp005876955	82.2788	783	1241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802235.1	s__Sinomonas humi	81.8744	749	1241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999765.1	s__Sinomonas mesophila	81.5284	692	1241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001577305.1	s__Sinomonas atrocyanea	81.4558	755	1241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	99.98	99.98	1.00	1.00	3	-
GCF_002224485.1	s__Sinomonas sp002224485	81.0095	690	1241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656475.1	s__Sinomonas sp014656475	80.7311	666	1241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:29,311] [INFO] GTDB search result was written to GCF_004919045.1_ASM491904v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:29,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:29,315] [INFO] DFAST_QC result json was written to GCF_004919045.1_ASM491904v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:29,315] [INFO] DFAST_QC completed!
[2024-01-24 14:40:29,315] [INFO] Total running time: 0h1m14s