[2023-06-28 23:06:07,305] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:06:07,309] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:06:07,309] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0bee0f8-c18c-4186-aab4-3b048f7f3399/dqc_reference
[2023-06-28 23:06:08,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:06:08,642] [INFO] Task started: Prodigal
[2023-06-28 23:06:08,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg089f08de-630c-4420-8d45-2ddddff48014/GCA_027320345.1_ASM2732034v1_genomic.fna.gz | prodigal -d GCA_027320345.1_ASM2732034v1_genomic.fna/cds.fna -a GCA_027320345.1_ASM2732034v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:06:16,157] [INFO] Task succeeded: Prodigal
[2023-06-28 23:06:16,158] [INFO] Task started: HMMsearch
[2023-06-28 23:06:16,158] [INFO] Running command: hmmsearch --tblout GCA_027320345.1_ASM2732034v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0bee0f8-c18c-4186-aab4-3b048f7f3399/dqc_reference/reference_markers.hmm GCA_027320345.1_ASM2732034v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:06:16,378] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:06:16,380] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg089f08de-630c-4420-8d45-2ddddff48014/GCA_027320345.1_ASM2732034v1_genomic.fna.gz]
[2023-06-28 23:06:16,408] [INFO] Query marker FASTA was written to GCA_027320345.1_ASM2732034v1_genomic.fna/markers.fasta
[2023-06-28 23:06:16,409] [INFO] Task started: Blastn
[2023-06-28 23:06:16,409] [INFO] Running command: blastn -query GCA_027320345.1_ASM2732034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0bee0f8-c18c-4186-aab4-3b048f7f3399/dqc_reference/reference_markers.fasta -out GCA_027320345.1_ASM2732034v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:06:16,981] [INFO] Task succeeded: Blastn
[2023-06-28 23:06:16,986] [INFO] Selected 19 target genomes.
[2023-06-28 23:06:16,986] [INFO] Target genome list was writen to GCA_027320345.1_ASM2732034v1_genomic.fna/target_genomes.txt
[2023-06-28 23:06:16,992] [INFO] Task started: fastANI
[2023-06-28 23:06:16,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg089f08de-630c-4420-8d45-2ddddff48014/GCA_027320345.1_ASM2732034v1_genomic.fna.gz --refList GCA_027320345.1_ASM2732034v1_genomic.fna/target_genomes.txt --output GCA_027320345.1_ASM2732034v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:06:32,160] [INFO] Task succeeded: fastANI
[2023-06-28 23:06:32,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0bee0f8-c18c-4186-aab4-3b048f7f3399/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:06:32,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0bee0f8-c18c-4186-aab4-3b048f7f3399/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:06:32,170] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:06:32,170] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:06:32,170] [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
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.7165	102	527	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	74.6753	89	527	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	74.6084	61	527	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	74.5692	70	527	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	74.5463	69	527	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	74.5436	70	527	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:06:32,172] [INFO] DFAST Taxonomy check result was written to GCA_027320345.1_ASM2732034v1_genomic.fna/tc_result.tsv
[2023-06-28 23:06:32,173] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:06:32,174] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:06:32,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0bee0f8-c18c-4186-aab4-3b048f7f3399/dqc_reference/checkm_data
[2023-06-28 23:06:32,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:06:32,200] [INFO] Task started: CheckM
[2023-06-28 23:06:32,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027320345.1_ASM2732034v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027320345.1_ASM2732034v1_genomic.fna/checkm_input GCA_027320345.1_ASM2732034v1_genomic.fna/checkm_result
[2023-06-28 23:06:58,025] [INFO] Task succeeded: CheckM
[2023-06-28 23:06:58,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 23:06:58,053] [INFO] ===== Completeness check finished =====
[2023-06-28 23:06:58,053] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:06:58,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027320345.1_ASM2732034v1_genomic.fna/markers.fasta)
[2023-06-28 23:06:58,054] [INFO] Task started: Blastn
[2023-06-28 23:06:58,054] [INFO] Running command: blastn -query GCA_027320345.1_ASM2732034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0bee0f8-c18c-4186-aab4-3b048f7f3399/dqc_reference/reference_markers_gtdb.fasta -out GCA_027320345.1_ASM2732034v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:06:58,656] [INFO] Task succeeded: Blastn
[2023-06-28 23:06:58,662] [INFO] Selected 16 target genomes.
[2023-06-28 23:06:58,662] [INFO] Target genome list was writen to GCA_027320345.1_ASM2732034v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:06:58,673] [INFO] Task started: fastANI
[2023-06-28 23:06:58,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg089f08de-630c-4420-8d45-2ddddff48014/GCA_027320345.1_ASM2732034v1_genomic.fna.gz --refList GCA_027320345.1_ASM2732034v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027320345.1_ASM2732034v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:07:05,885] [INFO] Task succeeded: fastANI
[2023-06-28 23:07:05,896] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:07:05,896] [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
GCA_002503985.1	s__UBA184 sp002503985	78.5748	146	527	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013290045.1	s__UBA184 sp013290045	78.5689	175	527	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495185.1	s__UBA184 sp002495185	77.7272	145	527	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013044425.1	s__UBA184 sp013044425	77.4918	101	527	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196675.1	s__Pseudonocardia dioxanivorans	74.6783	86	527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCF_003751265.1	s__Pseudokineococcus lusitanus	74.6229	81	527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:07:05,898] [INFO] GTDB search result was written to GCA_027320345.1_ASM2732034v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:07:05,899] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:07:05,902] [INFO] DFAST_QC result json was written to GCA_027320345.1_ASM2732034v1_genomic.fna/dqc_result.json
[2023-06-28 23:07:05,902] [INFO] DFAST_QC completed!
[2023-06-28 23:07:05,902] [INFO] Total running time: 0h0m59s