[2024-01-24 14:19:14,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:14,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:14,886] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f7cf602-5342-47e5-b984-e414f2918bf5/dqc_reference
[2024-01-24 14:19:16,045] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:16,046] [INFO] Task started: Prodigal
[2024-01-24 14:19:16,046] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3739817-4dd6-4686-801d-dcd73e6cd05a/GCF_004134905.2_ASM413490v2_genomic.fna.gz | prodigal -d GCF_004134905.2_ASM413490v2_genomic.fna/cds.fna -a GCF_004134905.2_ASM413490v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:27,633] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:27,633] [INFO] Task started: HMMsearch
[2024-01-24 14:19:27,633] [INFO] Running command: hmmsearch --tblout GCF_004134905.2_ASM413490v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f7cf602-5342-47e5-b984-e414f2918bf5/dqc_reference/reference_markers.hmm GCF_004134905.2_ASM413490v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:27,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:27,863] [INFO] Found 6/6 markers.
[2024-01-24 14:19:27,906] [INFO] Query marker FASTA was written to GCF_004134905.2_ASM413490v2_genomic.fna/markers.fasta
[2024-01-24 14:19:27,906] [INFO] Task started: Blastn
[2024-01-24 14:19:27,906] [INFO] Running command: blastn -query GCF_004134905.2_ASM413490v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f7cf602-5342-47e5-b984-e414f2918bf5/dqc_reference/reference_markers.fasta -out GCF_004134905.2_ASM413490v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:29,011] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:29,013] [INFO] Selected 10 target genomes.
[2024-01-24 14:19:29,014] [INFO] Target genome list was writen to GCF_004134905.2_ASM413490v2_genomic.fna/target_genomes.txt
[2024-01-24 14:19:29,018] [INFO] Task started: fastANI
[2024-01-24 14:19:29,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3739817-4dd6-4686-801d-dcd73e6cd05a/GCF_004134905.2_ASM413490v2_genomic.fna.gz --refList GCF_004134905.2_ASM413490v2_genomic.fna/target_genomes.txt --output GCF_004134905.2_ASM413490v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:37,745] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:37,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f7cf602-5342-47e5-b984-e414f2918bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:37,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f7cf602-5342-47e5-b984-e414f2918bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:37,754] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:37,755] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:37,755] [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
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	100.0	1332	1332	95	conclusive
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	83.4628	807	1332	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	82.9858	754	1332	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	82.9629	752	1332	95	below_threshold
Aeromicrobium yanjiei	strain=MF47	GCA_009649075.1	2662028	2662028	type	True	82.9563	738	1332	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	82.7564	764	1332	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	78.6431	416	1332	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	78.5071	407	1332	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	78.2887	423	1332	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.2564	465	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:37,756] [INFO] DFAST Taxonomy check result was written to GCF_004134905.2_ASM413490v2_genomic.fna/tc_result.tsv
[2024-01-24 14:19:37,757] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:37,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:37,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f7cf602-5342-47e5-b984-e414f2918bf5/dqc_reference/checkm_data
[2024-01-24 14:19:37,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:37,797] [INFO] Task started: CheckM
[2024-01-24 14:19:37,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004134905.2_ASM413490v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004134905.2_ASM413490v2_genomic.fna/checkm_input GCF_004134905.2_ASM413490v2_genomic.fna/checkm_result
[2024-01-24 14:20:41,630] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:41,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:41,650] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:41,651] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:41,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004134905.2_ASM413490v2_genomic.fna/markers.fasta)
[2024-01-24 14:20:41,651] [INFO] Task started: Blastn
[2024-01-24 14:20:41,651] [INFO] Running command: blastn -query GCF_004134905.2_ASM413490v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f7cf602-5342-47e5-b984-e414f2918bf5/dqc_reference/reference_markers_gtdb.fasta -out GCF_004134905.2_ASM413490v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:43,472] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:43,476] [INFO] Selected 7 target genomes.
[2024-01-24 14:20:43,476] [INFO] Target genome list was writen to GCF_004134905.2_ASM413490v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:43,487] [INFO] Task started: fastANI
[2024-01-24 14:20:43,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3739817-4dd6-4686-801d-dcd73e6cd05a/GCF_004134905.2_ASM413490v2_genomic.fna.gz --refList GCF_004134905.2_ASM413490v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004134905.2_ASM413490v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:50,328] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:50,335] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:50,335] [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_004134905.2	s__Aeromicrobium ginsengisoli	100.0	1332	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001425755.1	s__Aeromicrobium sp001425755	92.1053	1071	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428805.1	s__Aeromicrobium sp001428805	90.3379	1080	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506105.1	s__Aeromicrobium sp902506105	88.2324	1028	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283745.1	s__Aeromicrobium sp013283745	83.4516	808	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443875.1	s__Aeromicrobium sp003443875	83.4067	751	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426485.1	s__Aeromicrobium sp001426485	82.9276	777	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.44	97.44	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:50,336] [INFO] GTDB search result was written to GCF_004134905.2_ASM413490v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:50,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:50,340] [INFO] DFAST_QC result json was written to GCF_004134905.2_ASM413490v2_genomic.fna/dqc_result.json
[2024-01-24 14:20:50,340] [INFO] DFAST_QC completed!
[2024-01-24 14:20:50,340] [INFO] Total running time: 0h1m35s