[2024-01-24 13:28:01,245] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,252] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg65ebb2db-6014-4b50-a8d2-5db6338797e9/dqc_reference
[2024-01-24 13:28:02,552] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:02,553] [INFO] Task started: Prodigal
[2024-01-24 13:28:02,553] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ce1cde7-6ea9-42ec-9b4c-e632fd964180/GCF_000470775.1_ASM47077v1_genomic.fna.gz | prodigal -d GCF_000470775.1_ASM47077v1_genomic.fna/cds.fna -a GCF_000470775.1_ASM47077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:10,393] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:10,394] [INFO] Task started: HMMsearch
[2024-01-24 13:28:10,394] [INFO] Running command: hmmsearch --tblout GCF_000470775.1_ASM47077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65ebb2db-6014-4b50-a8d2-5db6338797e9/dqc_reference/reference_markers.hmm GCF_000470775.1_ASM47077v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:10,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:10,587] [INFO] Found 6/6 markers.
[2024-01-24 13:28:10,613] [INFO] Query marker FASTA was written to GCF_000470775.1_ASM47077v1_genomic.fna/markers.fasta
[2024-01-24 13:28:10,613] [INFO] Task started: Blastn
[2024-01-24 13:28:10,614] [INFO] Running command: blastn -query GCF_000470775.1_ASM47077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ebb2db-6014-4b50-a8d2-5db6338797e9/dqc_reference/reference_markers.fasta -out GCF_000470775.1_ASM47077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:11,808] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:11,812] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:11,812] [INFO] Target genome list was writen to GCF_000470775.1_ASM47077v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:11,841] [INFO] Task started: fastANI
[2024-01-24 13:28:11,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ce1cde7-6ea9-42ec-9b4c-e632fd964180/GCF_000470775.1_ASM47077v1_genomic.fna.gz --refList GCF_000470775.1_ASM47077v1_genomic.fna/target_genomes.txt --output GCF_000470775.1_ASM47077v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:23,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:23,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65ebb2db-6014-4b50-a8d2-5db6338797e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:23,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65ebb2db-6014-4b50-a8d2-5db6338797e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:23,319] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:23,319] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:23,319] [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
Leifsonia xyli subsp. cynodontis	strain=DSM 46306	GCA_000470775.1	31966	1575	type	True	100.0	890	895	95	conclusive
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	82.5968	560	895	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	82.0415	424	895	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	81.8848	509	895	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	81.8842	554	895	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	81.7168	569	895	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	79.0851	282	895	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.0545	324	895	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.8665	296	895	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.7481	305	895	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.6868	290	895	95	below_threshold
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	78.6049	297	895	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.5501	327	895	95	below_threshold
Clavibacter michiganensis	strain=VKM Ac-1403	GCA_900168345.1	28447	28447	suspected-type	True	78.5427	294	895	95	below_threshold
Cryobacterium aureum	strain=Hh31	GCA_002954245.1	995037	995037	type	True	77.3945	218	895	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:23,321] [INFO] DFAST Taxonomy check result was written to GCF_000470775.1_ASM47077v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:23,321] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:23,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:23,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65ebb2db-6014-4b50-a8d2-5db6338797e9/dqc_reference/checkm_data
[2024-01-24 13:28:23,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:23,349] [INFO] Task started: CheckM
[2024-01-24 13:28:23,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000470775.1_ASM47077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000470775.1_ASM47077v1_genomic.fna/checkm_input GCF_000470775.1_ASM47077v1_genomic.fna/checkm_result
[2024-01-24 13:28:50,762] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:50,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:50,783] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:50,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:50,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000470775.1_ASM47077v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:50,784] [INFO] Task started: Blastn
[2024-01-24 13:28:50,784] [INFO] Running command: blastn -query GCF_000470775.1_ASM47077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ebb2db-6014-4b50-a8d2-5db6338797e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000470775.1_ASM47077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:52,488] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:52,492] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:52,492] [INFO] Target genome list was writen to GCF_000470775.1_ASM47077v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:52,509] [INFO] Task started: fastANI
[2024-01-24 13:28:52,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ce1cde7-6ea9-42ec-9b4c-e632fd964180/GCF_000470775.1_ASM47077v1_genomic.fna.gz --refList GCF_000470775.1_ASM47077v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000470775.1_ASM47077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:03,439] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:03,450] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:03,450] [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_000470775.1	s__Leifsonia cynodontis	100.0	888	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000007665.1	s__Leifsonia xyli_C	92.4548	711	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013410375.1	s__Leifsonia shinshuensis	82.5756	562	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217625.1	s__Leifsonia shinshuensis_A	82.4081	553	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664105.1	s__Leifsonia sp003664105	82.1659	514	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898805.1	s__Leifsonia sp001898805	82.01	539	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408745.1	s__Leifsonia soli	81.885	509	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.25	98.25	0.89	0.89	2	-
GCF_013359685.1	s__Leifsonia sp013359685	81.8651	526	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003367665.1	s__Leifsonia sp003367665	81.8206	536	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423695.1	s__Leifsonia sp001423695	81.753	541	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190775.1	s__Leifsonia aquatica	81.7426	567	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCF_000633535.1	s__Leifsonia aquatica_A	81.6891	532	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765225.1	s__Leifsonia sp009765225	81.0632	494	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:03,455] [INFO] GTDB search result was written to GCF_000470775.1_ASM47077v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:03,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:03,462] [INFO] DFAST_QC result json was written to GCF_000470775.1_ASM47077v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:03,463] [INFO] DFAST_QC completed!
[2024-01-24 13:29:03,463] [INFO] Total running time: 0h1m2s