[2024-01-24 14:47:03,859] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:03,861] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:03,861] [INFO] DQC Reference Directory: /var/lib/cwl/stg856a43a5-d236-4022-b6b5-5a105114f969/dqc_reference
[2024-01-24 14:47:05,069] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:05,070] [INFO] Task started: Prodigal
[2024-01-24 14:47:05,070] [INFO] Running command: gunzip -c /var/lib/cwl/stgf927b97a-7b52-48a4-b7c0-fa18ce862716/GCF_003586285.1_ASM358628v1_genomic.fna.gz | prodigal -d GCF_003586285.1_ASM358628v1_genomic.fna/cds.fna -a GCF_003586285.1_ASM358628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:16,701] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:16,702] [INFO] Task started: HMMsearch
[2024-01-24 14:47:16,702] [INFO] Running command: hmmsearch --tblout GCF_003586285.1_ASM358628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg856a43a5-d236-4022-b6b5-5a105114f969/dqc_reference/reference_markers.hmm GCF_003586285.1_ASM358628v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:16,987] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:16,988] [INFO] Found 6/6 markers.
[2024-01-24 14:47:17,025] [INFO] Query marker FASTA was written to GCF_003586285.1_ASM358628v1_genomic.fna/markers.fasta
[2024-01-24 14:47:17,025] [INFO] Task started: Blastn
[2024-01-24 14:47:17,025] [INFO] Running command: blastn -query GCF_003586285.1_ASM358628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg856a43a5-d236-4022-b6b5-5a105114f969/dqc_reference/reference_markers.fasta -out GCF_003586285.1_ASM358628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:18,320] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:18,326] [INFO] Selected 11 target genomes.
[2024-01-24 14:47:18,327] [INFO] Target genome list was writen to GCF_003586285.1_ASM358628v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:18,345] [INFO] Task started: fastANI
[2024-01-24 14:47:18,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgf927b97a-7b52-48a4-b7c0-fa18ce862716/GCF_003586285.1_ASM358628v1_genomic.fna.gz --refList GCF_003586285.1_ASM358628v1_genomic.fna/target_genomes.txt --output GCF_003586285.1_ASM358628v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:29,443] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:29,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg856a43a5-d236-4022-b6b5-5a105114f969/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:29,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg856a43a5-d236-4022-b6b5-5a105114f969/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:29,454] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:29,455] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:29,455] [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 endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	100.0	1340	1340	95	conclusive
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	87.4905	977	1340	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	84.8755	859	1340	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	83.9638	822	1340	95	below_threshold
Aeromicrobium yanjiei	strain=MF47	GCA_009649075.1	2662028	2662028	type	True	83.9348	804	1340	95	below_threshold
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	82.7529	766	1340	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	78.2241	452	1340	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.214	485	1340	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	78.0281	393	1340	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	78.0199	483	1340	95	below_threshold
Kineococcus rhizosphaerae	strain=DSM 19711	GCA_003002055.1	559628	559628	type	True	76.4742	375	1340	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:29,457] [INFO] DFAST Taxonomy check result was written to GCF_003586285.1_ASM358628v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:29,458] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:29,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:29,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg856a43a5-d236-4022-b6b5-5a105114f969/dqc_reference/checkm_data
[2024-01-24 14:47:29,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:29,509] [INFO] Task started: CheckM
[2024-01-24 14:47:29,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003586285.1_ASM358628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003586285.1_ASM358628v1_genomic.fna/checkm_input GCF_003586285.1_ASM358628v1_genomic.fna/checkm_result
[2024-01-24 14:48:36,329] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:36,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:36,352] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:36,352] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:36,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003586285.1_ASM358628v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:36,353] [INFO] Task started: Blastn
[2024-01-24 14:48:36,353] [INFO] Running command: blastn -query GCF_003586285.1_ASM358628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg856a43a5-d236-4022-b6b5-5a105114f969/dqc_reference/reference_markers_gtdb.fasta -out GCF_003586285.1_ASM358628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:38,299] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:38,303] [INFO] Selected 7 target genomes.
[2024-01-24 14:48:38,303] [INFO] Target genome list was writen to GCF_003586285.1_ASM358628v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:38,310] [INFO] Task started: fastANI
[2024-01-24 14:48:38,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgf927b97a-7b52-48a4-b7c0-fa18ce862716/GCF_003586285.1_ASM358628v1_genomic.fna.gz --refList GCF_003586285.1_ASM358628v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003586285.1_ASM358628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:45,489] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:45,503] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:45,503] [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_003586285.1	s__Aeromicrobium endophyticum	100.0	1340	1340	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_001426485.1	s__Aeromicrobium sp001426485	87.7376	1003	1340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.44	97.44	0.91	0.91	2	-
GCF_017876595.1	s__Aeromicrobium fastidiosum	87.4772	978	1340	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	84.8663	860	1340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003065605.1	s__Aeromicrobium chenweiae	84.0097	818	1340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009649075.1	s__Aeromicrobium yanjiei	83.9581	802	1340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.81	98.81	0.96	0.95	3	-
GCF_004134905.2	s__Aeromicrobium ginsengisoli	82.726	768	1340	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 14:48:45,507] [INFO] GTDB search result was written to GCF_003586285.1_ASM358628v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:45,508] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:45,512] [INFO] DFAST_QC result json was written to GCF_003586285.1_ASM358628v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:45,512] [INFO] DFAST_QC completed!
[2024-01-24 14:48:45,512] [INFO] Total running time: 0h1m42s