[2024-01-24 12:21:35,978] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:36,122] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:36,123] [INFO] DQC Reference Directory: /var/lib/cwl/stgb87b4524-0164-4cfd-ac4d-40cdfa9139bf/dqc_reference
[2024-01-24 12:21:37,353] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:37,354] [INFO] Task started: Prodigal
[2024-01-24 12:21:37,354] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c83fba5-9fec-45e6-a27a-97b5a5946067/GCF_003627075.1_ASM362707v1_genomic.fna.gz | prodigal -d GCF_003627075.1_ASM362707v1_genomic.fna/cds.fna -a GCF_003627075.1_ASM362707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:46,199] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:46,199] [INFO] Task started: HMMsearch
[2024-01-24 12:21:46,200] [INFO] Running command: hmmsearch --tblout GCF_003627075.1_ASM362707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb87b4524-0164-4cfd-ac4d-40cdfa9139bf/dqc_reference/reference_markers.hmm GCF_003627075.1_ASM362707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:46,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:46,456] [INFO] Found 6/6 markers.
[2024-01-24 12:21:46,489] [INFO] Query marker FASTA was written to GCF_003627075.1_ASM362707v1_genomic.fna/markers.fasta
[2024-01-24 12:21:46,490] [INFO] Task started: Blastn
[2024-01-24 12:21:46,490] [INFO] Running command: blastn -query GCF_003627075.1_ASM362707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87b4524-0164-4cfd-ac4d-40cdfa9139bf/dqc_reference/reference_markers.fasta -out GCF_003627075.1_ASM362707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:47,766] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:47,770] [INFO] Selected 22 target genomes.
[2024-01-24 12:21:47,771] [INFO] Target genome list was writen to GCF_003627075.1_ASM362707v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:47,801] [INFO] Task started: fastANI
[2024-01-24 12:21:47,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c83fba5-9fec-45e6-a27a-97b5a5946067/GCF_003627075.1_ASM362707v1_genomic.fna.gz --refList GCF_003627075.1_ASM362707v1_genomic.fna/target_genomes.txt --output GCF_003627075.1_ASM362707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:03,100] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:03,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb87b4524-0164-4cfd-ac4d-40cdfa9139bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:03,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb87b4524-0164-4cfd-ac4d-40cdfa9139bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:03,120] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:03,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:03,120] [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	100.0	1032	1032	95	conclusive
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	85.2342	653	1032	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	80.1489	424	1032	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	80.0558	438	1032	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.7717	523	1032	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	79.7575	502	1032	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	79.7138	518	1032	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.7017	454	1032	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.4987	506	1032	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	79.4426	524	1032	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	79.3457	474	1032	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	79.2774	445	1032	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	79.272	468	1032	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	79.2611	420	1032	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	79.1912	446	1032	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.1546	433	1032	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.1161	449	1032	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	79.1127	425	1032	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.1074	430	1032	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	78.7937	420	1032	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	78.5362	390	1032	95	below_threshold
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	77.2565	317	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:03,122] [INFO] DFAST Taxonomy check result was written to GCF_003627075.1_ASM362707v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:03,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:03,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:03,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb87b4524-0164-4cfd-ac4d-40cdfa9139bf/dqc_reference/checkm_data
[2024-01-24 12:22:03,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:03,158] [INFO] Task started: CheckM
[2024-01-24 12:22:03,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003627075.1_ASM362707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003627075.1_ASM362707v1_genomic.fna/checkm_input GCF_003627075.1_ASM362707v1_genomic.fna/checkm_result
[2024-01-24 12:22:49,164] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:49,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:49,190] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:49,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:49,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003627075.1_ASM362707v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:49,191] [INFO] Task started: Blastn
[2024-01-24 12:22:49,192] [INFO] Running command: blastn -query GCF_003627075.1_ASM362707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87b4524-0164-4cfd-ac4d-40cdfa9139bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_003627075.1_ASM362707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:51,348] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:51,356] [INFO] Selected 7 target genomes.
[2024-01-24 12:22:51,357] [INFO] Target genome list was writen to GCF_003627075.1_ASM362707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:51,363] [INFO] Task started: fastANI
[2024-01-24 12:22:51,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c83fba5-9fec-45e6-a27a-97b5a5946067/GCF_003627075.1_ASM362707v1_genomic.fna.gz --refList GCF_003627075.1_ASM362707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003627075.1_ASM362707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:57,378] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:57,385] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:57,386] [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	100.0	1032	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001898835.1	s__Protaetiibacter sp001898835	86.2969	731	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014483895.1	s__Protaetiibacter sp014483895	85.7763	738	1032	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	85.5411	678	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	85.4794	640	1032	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	85.247	652	1032	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	85.1398	705	1032	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 12:22:57,388] [INFO] GTDB search result was written to GCF_003627075.1_ASM362707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:57,389] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:57,393] [INFO] DFAST_QC result json was written to GCF_003627075.1_ASM362707v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:57,393] [INFO] DFAST_QC completed!
[2024-01-24 12:22:57,393] [INFO] Total running time: 0h1m21s