[2024-01-24 13:49:55,326] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,328] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,328] [INFO] DQC Reference Directory: /var/lib/cwl/stg20e36d21-f458-4d02-af54-9b41ec3aa7c6/dqc_reference
[2024-01-24 13:49:56,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,552] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,552] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b189a02-51d9-478a-a7aa-9672134766d0/GCF_009649075.1_ASM964907v1_genomic.fna.gz | prodigal -d GCF_009649075.1_ASM964907v1_genomic.fna/cds.fna -a GCF_009649075.1_ASM964907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:07,185] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:07,186] [INFO] Task started: HMMsearch
[2024-01-24 13:50:07,186] [INFO] Running command: hmmsearch --tblout GCF_009649075.1_ASM964907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20e36d21-f458-4d02-af54-9b41ec3aa7c6/dqc_reference/reference_markers.hmm GCF_009649075.1_ASM964907v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:07,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:07,445] [INFO] Found 6/6 markers.
[2024-01-24 13:50:07,479] [INFO] Query marker FASTA was written to GCF_009649075.1_ASM964907v1_genomic.fna/markers.fasta
[2024-01-24 13:50:07,479] [INFO] Task started: Blastn
[2024-01-24 13:50:07,480] [INFO] Running command: blastn -query GCF_009649075.1_ASM964907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e36d21-f458-4d02-af54-9b41ec3aa7c6/dqc_reference/reference_markers.fasta -out GCF_009649075.1_ASM964907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:08,676] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:08,681] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:08,681] [INFO] Target genome list was writen to GCF_009649075.1_ASM964907v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:08,709] [INFO] Task started: fastANI
[2024-01-24 13:50:08,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b189a02-51d9-478a-a7aa-9672134766d0/GCF_009649075.1_ASM964907v1_genomic.fna.gz --refList GCF_009649075.1_ASM964907v1_genomic.fna/target_genomes.txt --output GCF_009649075.1_ASM964907v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:17,568] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:17,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20e36d21-f458-4d02-af54-9b41ec3aa7c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:17,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20e36d21-f458-4d02-af54-9b41ec3aa7c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:17,582] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:17,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:17,583] [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 yanjiei	strain=MF47	GCA_009649075.1	2662028	2662028	type	True	100.0	1227	1227	95	conclusive
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	88.0436	985	1227	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	85.4046	828	1227	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	84.0352	798	1227	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	84.027	785	1227	95	below_threshold
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	82.963	722	1227	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	78.5426	389	1227	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	78.4401	409	1227	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.342	439	1227	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	78.2752	355	1227	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,584] [INFO] DFAST Taxonomy check result was written to GCF_009649075.1_ASM964907v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:17,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:17,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:17,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20e36d21-f458-4d02-af54-9b41ec3aa7c6/dqc_reference/checkm_data
[2024-01-24 13:50:17,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:17,626] [INFO] Task started: CheckM
[2024-01-24 13:50:17,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009649075.1_ASM964907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009649075.1_ASM964907v1_genomic.fna/checkm_input GCF_009649075.1_ASM964907v1_genomic.fna/checkm_result
[2024-01-24 13:51:26,591] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:26,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:26,622] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:26,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:26,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009649075.1_ASM964907v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:26,624] [INFO] Task started: Blastn
[2024-01-24 13:51:26,624] [INFO] Running command: blastn -query GCF_009649075.1_ASM964907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e36d21-f458-4d02-af54-9b41ec3aa7c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009649075.1_ASM964907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:28,461] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:28,465] [INFO] Selected 7 target genomes.
[2024-01-24 13:51:28,465] [INFO] Target genome list was writen to GCF_009649075.1_ASM964907v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:28,502] [INFO] Task started: fastANI
[2024-01-24 13:51:28,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b189a02-51d9-478a-a7aa-9672134766d0/GCF_009649075.1_ASM964907v1_genomic.fna.gz --refList GCF_009649075.1_ASM964907v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009649075.1_ASM964907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:35,179] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:35,192] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:35,193] [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_009649075.1	s__Aeromicrobium yanjiei	100.0	1227	1227	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.81	98.81	0.96	0.95	3	conclusive
GCF_003065605.1	s__Aeromicrobium chenweiae	88.0548	986	1227	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013283745.1	s__Aeromicrobium sp013283745	85.3879	829	1227	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	84.2773	817	1227	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.44	97.44	0.91	0.91	2	-
GCF_003586285.1	s__Aeromicrobium endophyticum	84.0563	796	1227	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876595.1	s__Aeromicrobium fastidiosum	84.0327	785	1227	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425755.1	s__Aeromicrobium sp001425755	83.1416	713	1227	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:35,194] [INFO] GTDB search result was written to GCF_009649075.1_ASM964907v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:35,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:35,198] [INFO] DFAST_QC result json was written to GCF_009649075.1_ASM964907v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:35,198] [INFO] DFAST_QC completed!
[2024-01-24 13:51:35,198] [INFO] Total running time: 0h1m40s