[2024-01-24 12:23:03,287] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,289] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b837e5f-1788-43b1-a17a-cc2c0bd60a84/dqc_reference
[2024-01-24 12:23:04,608] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,609] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,610] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9cf2fea-bbc8-4864-b65f-6b21a24bd67f/GCF_024752305.1_ASM2475230v1_genomic.fna.gz | prodigal -d GCF_024752305.1_ASM2475230v1_genomic.fna/cds.fna -a GCF_024752305.1_ASM2475230v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:13,172] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:13,173] [INFO] Task started: HMMsearch
[2024-01-24 12:23:13,173] [INFO] Running command: hmmsearch --tblout GCF_024752305.1_ASM2475230v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b837e5f-1788-43b1-a17a-cc2c0bd60a84/dqc_reference/reference_markers.hmm GCF_024752305.1_ASM2475230v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:13,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:13,462] [INFO] Found 6/6 markers.
[2024-01-24 12:23:13,499] [INFO] Query marker FASTA was written to GCF_024752305.1_ASM2475230v1_genomic.fna/markers.fasta
[2024-01-24 12:23:13,500] [INFO] Task started: Blastn
[2024-01-24 12:23:13,500] [INFO] Running command: blastn -query GCF_024752305.1_ASM2475230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b837e5f-1788-43b1-a17a-cc2c0bd60a84/dqc_reference/reference_markers.fasta -out GCF_024752305.1_ASM2475230v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:14,894] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:14,898] [INFO] Selected 23 target genomes.
[2024-01-24 12:23:14,899] [INFO] Target genome list was writen to GCF_024752305.1_ASM2475230v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:14,907] [INFO] Task started: fastANI
[2024-01-24 12:23:14,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9cf2fea-bbc8-4864-b65f-6b21a24bd67f/GCF_024752305.1_ASM2475230v1_genomic.fna.gz --refList GCF_024752305.1_ASM2475230v1_genomic.fna/target_genomes.txt --output GCF_024752305.1_ASM2475230v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:29,791] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:29,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b837e5f-1788-43b1-a17a-cc2c0bd60a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:29,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b837e5f-1788-43b1-a17a-cc2c0bd60a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:29,809] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:29,810] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:29,810] [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
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	85.7362	726	987	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	84.3372	620	987	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.6359	527	987	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	79.4059	482	987	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.3725	482	987	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	79.3662	509	987	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	79.2725	397	987	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.1125	394	987	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.0077	410	987	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.9871	412	987	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	78.9541	456	987	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	78.9448	421	987	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	78.9073	365	987	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.8967	415	987	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	78.8209	420	987	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=LMG 3663	GCA_002240565.1	33014	28447	type	True	78.8156	421	987	95	below_threshold
Agrococcus terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	78.7598	429	987	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	78.7377	411	987	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	78.7332	369	987	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.7304	418	987	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.7266	394	987	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	78.3805	357	987	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	78.3563	351	987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,812] [INFO] DFAST Taxonomy check result was written to GCF_024752305.1_ASM2475230v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:29,812] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:29,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:29,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b837e5f-1788-43b1-a17a-cc2c0bd60a84/dqc_reference/checkm_data
[2024-01-24 12:23:29,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:29,848] [INFO] Task started: CheckM
[2024-01-24 12:23:29,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024752305.1_ASM2475230v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024752305.1_ASM2475230v1_genomic.fna/checkm_input GCF_024752305.1_ASM2475230v1_genomic.fna/checkm_result
[2024-01-24 12:23:59,757] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:59,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:59,780] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:59,781] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:59,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024752305.1_ASM2475230v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:59,782] [INFO] Task started: Blastn
[2024-01-24 12:23:59,782] [INFO] Running command: blastn -query GCF_024752305.1_ASM2475230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b837e5f-1788-43b1-a17a-cc2c0bd60a84/dqc_reference/reference_markers_gtdb.fasta -out GCF_024752305.1_ASM2475230v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:01,817] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:01,822] [INFO] Selected 7 target genomes.
[2024-01-24 12:24:01,823] [INFO] Target genome list was writen to GCF_024752305.1_ASM2475230v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:01,830] [INFO] Task started: fastANI
[2024-01-24 12:24:01,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9cf2fea-bbc8-4864-b65f-6b21a24bd67f/GCF_024752305.1_ASM2475230v1_genomic.fna.gz --refList GCF_024752305.1_ASM2475230v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024752305.1_ASM2475230v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:07,302] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:07,313] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:07,313] [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_003627075.1	s__Protaetiibacter intestinalis	85.7519	725	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014483895.1	s__Protaetiibacter sp014483895	85.5561	710	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898835.1	s__Protaetiibacter sp001898835	85.5224	741	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003852775.1	s__Protaetiibacter sp003852775	85.095	619	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243275.1	s__Protaetiibacter sp003243275	85.0668	666	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365275.1	s__Protaetiibacter larvae	84.3176	622	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216815.1	s__Protaetiibacter sp004216815	84.2601	730	987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:07,315] [INFO] GTDB search result was written to GCF_024752305.1_ASM2475230v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:07,316] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:07,319] [INFO] DFAST_QC result json was written to GCF_024752305.1_ASM2475230v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:07,319] [INFO] DFAST_QC completed!
[2024-01-24 12:24:07,319] [INFO] Total running time: 0h1m4s