[2023-06-30 01:12:07,089] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:12:07,091] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:12:07,092] [INFO] DQC Reference Directory: /var/lib/cwl/stga5dcf71e-22ce-4854-845f-48c3425c0268/dqc_reference
[2023-06-30 01:12:08,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:12:08,381] [INFO] Task started: Prodigal
[2023-06-30 01:12:08,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c0d4572-3b31-4642-9686-7a9f94a641fc/GCA_024653355.1_ASM2465335v1_genomic.fna.gz | prodigal -d GCA_024653355.1_ASM2465335v1_genomic.fna/cds.fna -a GCA_024653355.1_ASM2465335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:12:13,550] [INFO] Task succeeded: Prodigal
[2023-06-30 01:12:13,551] [INFO] Task started: HMMsearch
[2023-06-30 01:12:13,551] [INFO] Running command: hmmsearch --tblout GCA_024653355.1_ASM2465335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5dcf71e-22ce-4854-845f-48c3425c0268/dqc_reference/reference_markers.hmm GCA_024653355.1_ASM2465335v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:12:13,816] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:12:13,817] [INFO] Found 6/6 markers.
[2023-06-30 01:12:13,851] [INFO] Query marker FASTA was written to GCA_024653355.1_ASM2465335v1_genomic.fna/markers.fasta
[2023-06-30 01:12:13,851] [INFO] Task started: Blastn
[2023-06-30 01:12:13,851] [INFO] Running command: blastn -query GCA_024653355.1_ASM2465335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5dcf71e-22ce-4854-845f-48c3425c0268/dqc_reference/reference_markers.fasta -out GCA_024653355.1_ASM2465335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:12:14,457] [INFO] Task succeeded: Blastn
[2023-06-30 01:12:14,461] [INFO] Selected 10 target genomes.
[2023-06-30 01:12:14,461] [INFO] Target genome list was writen to GCA_024653355.1_ASM2465335v1_genomic.fna/target_genomes.txt
[2023-06-30 01:12:14,462] [INFO] Task started: fastANI
[2023-06-30 01:12:14,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0d4572-3b31-4642-9686-7a9f94a641fc/GCA_024653355.1_ASM2465335v1_genomic.fna.gz --refList GCA_024653355.1_ASM2465335v1_genomic.fna/target_genomes.txt --output GCA_024653355.1_ASM2465335v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:12:19,890] [INFO] Task succeeded: fastANI
[2023-06-30 01:12:19,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5dcf71e-22ce-4854-845f-48c3425c0268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:12:19,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5dcf71e-22ce-4854-845f-48c3425c0268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:12:19,893] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:12:19,893] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 01:12:19,894] [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
--------------------------------------------------------------------------------
[2023-06-30 01:12:19,896] [INFO] DFAST Taxonomy check result was written to GCA_024653355.1_ASM2465335v1_genomic.fna/tc_result.tsv
[2023-06-30 01:12:19,897] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:12:19,897] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:12:19,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5dcf71e-22ce-4854-845f-48c3425c0268/dqc_reference/checkm_data
[2023-06-30 01:12:19,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:12:19,930] [INFO] Task started: CheckM
[2023-06-30 01:12:19,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024653355.1_ASM2465335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024653355.1_ASM2465335v1_genomic.fna/checkm_input GCA_024653355.1_ASM2465335v1_genomic.fna/checkm_result
[2023-06-30 01:12:42,190] [INFO] Task succeeded: CheckM
[2023-06-30 01:12:42,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 01:12:42,213] [INFO] ===== Completeness check finished =====
[2023-06-30 01:12:42,213] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:12:42,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024653355.1_ASM2465335v1_genomic.fna/markers.fasta)
[2023-06-30 01:12:42,214] [INFO] Task started: Blastn
[2023-06-30 01:12:42,214] [INFO] Running command: blastn -query GCA_024653355.1_ASM2465335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5dcf71e-22ce-4854-845f-48c3425c0268/dqc_reference/reference_markers_gtdb.fasta -out GCA_024653355.1_ASM2465335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:12:43,054] [INFO] Task succeeded: Blastn
[2023-06-30 01:12:43,059] [INFO] Selected 14 target genomes.
[2023-06-30 01:12:43,059] [INFO] Target genome list was writen to GCA_024653355.1_ASM2465335v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:12:43,069] [INFO] Task started: fastANI
[2023-06-30 01:12:43,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0d4572-3b31-4642-9686-7a9f94a641fc/GCA_024653355.1_ASM2465335v1_genomic.fna.gz --refList GCA_024653355.1_ASM2465335v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024653355.1_ASM2465335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:12:49,162] [INFO] Task succeeded: fastANI
[2023-06-30 01:12:49,166] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 01:12:49,167] [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_013177935.1	s__JABLXZ01 sp013177935	83.3821	535	623	d__Bacteria;p__WOR-3;c__WOR-3;o__UBA2258;f__UBA2258;g__JABLXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051175.1	s__DTMZ01 sp011051175	77.5957	80	623	d__Bacteria;p__WOR-3;c__WOR-3;o__UBA2258;f__UBA2258;g__DTMZ01	95.0	100.00	100.00	0.99	0.99	2	-
GCA_011355155.1	s__DTMZ01 sp011355155	77.1831	72	623	d__Bacteria;p__WOR-3;c__WOR-3;o__UBA2258;f__UBA2258;g__DTMZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 01:12:49,169] [INFO] GTDB search result was written to GCA_024653355.1_ASM2465335v1_genomic.fna/result_gtdb.tsv
[2023-06-30 01:12:49,169] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:12:49,172] [INFO] DFAST_QC result json was written to GCA_024653355.1_ASM2465335v1_genomic.fna/dqc_result.json
[2023-06-30 01:12:49,172] [INFO] DFAST_QC completed!
[2023-06-30 01:12:49,172] [INFO] Total running time: 0h0m42s