[2024-01-25 19:44:05,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:05,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:05,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b170b99-67a0-4ca1-8a09-04e03b51ac90/dqc_reference
[2024-01-25 19:44:06,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:06,818] [INFO] Task started: Prodigal
[2024-01-25 19:44:06,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaf39d1c-6bf2-4b10-bd43-87ae1cfd592e/GCF_017876595.1_ASM1787659v1_genomic.fna.gz | prodigal -d GCF_017876595.1_ASM1787659v1_genomic.fna/cds.fna -a GCF_017876595.1_ASM1787659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:17,707] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:17,707] [INFO] Task started: HMMsearch
[2024-01-25 19:44:17,707] [INFO] Running command: hmmsearch --tblout GCF_017876595.1_ASM1787659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b170b99-67a0-4ca1-8a09-04e03b51ac90/dqc_reference/reference_markers.hmm GCF_017876595.1_ASM1787659v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:17,939] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:17,940] [INFO] Found 6/6 markers.
[2024-01-25 19:44:17,977] [INFO] Query marker FASTA was written to GCF_017876595.1_ASM1787659v1_genomic.fna/markers.fasta
[2024-01-25 19:44:17,978] [INFO] Task started: Blastn
[2024-01-25 19:44:17,978] [INFO] Running command: blastn -query GCF_017876595.1_ASM1787659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b170b99-67a0-4ca1-8a09-04e03b51ac90/dqc_reference/reference_markers.fasta -out GCF_017876595.1_ASM1787659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:19,089] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:19,092] [INFO] Selected 10 target genomes.
[2024-01-25 19:44:19,093] [INFO] Target genome list was writen to GCF_017876595.1_ASM1787659v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:19,106] [INFO] Task started: fastANI
[2024-01-25 19:44:19,107] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaf39d1c-6bf2-4b10-bd43-87ae1cfd592e/GCF_017876595.1_ASM1787659v1_genomic.fna.gz --refList GCF_017876595.1_ASM1787659v1_genomic.fna/target_genomes.txt --output GCF_017876595.1_ASM1787659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:28,383] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:28,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b170b99-67a0-4ca1-8a09-04e03b51ac90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:28,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b170b99-67a0-4ca1-8a09-04e03b51ac90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:28,391] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:28,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:28,391] [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 fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	100.0	1308	1308	95	conclusive
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	87.414	969	1308	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	84.9155	884	1308	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	84.2086	814	1308	95	below_threshold
Aeromicrobium yanjiei	strain=MF47	GCA_009649075.1	2662028	2662028	type	True	84.0104	774	1308	95	below_threshold
Aeromicrobium phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	80.347	529	1308	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	78.2399	438	1308	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	78.0549	377	1308	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	77.9665	412	1308	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	77.8284	465	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:28,393] [INFO] DFAST Taxonomy check result was written to GCF_017876595.1_ASM1787659v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:28,393] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:28,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:28,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b170b99-67a0-4ca1-8a09-04e03b51ac90/dqc_reference/checkm_data
[2024-01-25 19:44:28,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:28,434] [INFO] Task started: CheckM
[2024-01-25 19:44:28,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876595.1_ASM1787659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876595.1_ASM1787659v1_genomic.fna/checkm_input GCF_017876595.1_ASM1787659v1_genomic.fna/checkm_result
[2024-01-25 19:45:40,174] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:40,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:40,190] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:40,191] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:40,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876595.1_ASM1787659v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:40,192] [INFO] Task started: Blastn
[2024-01-25 19:45:40,192] [INFO] Running command: blastn -query GCF_017876595.1_ASM1787659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b170b99-67a0-4ca1-8a09-04e03b51ac90/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876595.1_ASM1787659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:41,982] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:41,985] [INFO] Selected 7 target genomes.
[2024-01-25 19:45:41,985] [INFO] Target genome list was writen to GCF_017876595.1_ASM1787659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:41,990] [INFO] Task started: fastANI
[2024-01-25 19:45:41,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaf39d1c-6bf2-4b10-bd43-87ae1cfd592e/GCF_017876595.1_ASM1787659v1_genomic.fna.gz --refList GCF_017876595.1_ASM1787659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876595.1_ASM1787659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:48,849] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:48,855] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:48,855] [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_017876595.1	s__Aeromicrobium fastidiosum	100.0	1307	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001426485.1	s__Aeromicrobium sp001426485	87.4164	974	1308	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	87.4084	970	1308	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	84.9062	885	1308	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	84.2109	814	1308	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	84.0412	774	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.81	98.81	0.96	0.95	3	-
GCF_902506105.1	s__Aeromicrobium sp902506105	82.9553	784	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:48,856] [INFO] GTDB search result was written to GCF_017876595.1_ASM1787659v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:48,857] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:48,859] [INFO] DFAST_QC result json was written to GCF_017876595.1_ASM1787659v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:48,860] [INFO] DFAST_QC completed!
[2024-01-25 19:45:48,860] [INFO] Total running time: 0h1m43s