[2023-06-17 11:08:17,738] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:08:17,740] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:08:17,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbb29c8e-20b4-4909-9f5c-b9b182aabf12/dqc_reference
[2023-06-17 11:08:19,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:08:19,078] [INFO] Task started: Prodigal
[2023-06-17 11:08:19,078] [INFO] Running command: gunzip -c /var/lib/cwl/stgd31f4e09-c26c-4399-968d-b6870f5519f8/GCA_028680655.1_ASM2868065v1_genomic.fna.gz | prodigal -d GCA_028680655.1_ASM2868065v1_genomic.fna/cds.fna -a GCA_028680655.1_ASM2868065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:08:20,438] [INFO] Task succeeded: Prodigal
[2023-06-17 11:08:20,439] [INFO] Task started: HMMsearch
[2023-06-17 11:08:20,439] [INFO] Running command: hmmsearch --tblout GCA_028680655.1_ASM2868065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbb29c8e-20b4-4909-9f5c-b9b182aabf12/dqc_reference/reference_markers.hmm GCA_028680655.1_ASM2868065v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:08:20,641] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:08:20,643] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd31f4e09-c26c-4399-968d-b6870f5519f8/GCA_028680655.1_ASM2868065v1_genomic.fna.gz]
[2023-06-17 11:08:20,662] [INFO] Query marker FASTA was written to GCA_028680655.1_ASM2868065v1_genomic.fna/markers.fasta
[2023-06-17 11:08:20,662] [INFO] Task started: Blastn
[2023-06-17 11:08:20,662] [INFO] Running command: blastn -query GCA_028680655.1_ASM2868065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbb29c8e-20b4-4909-9f5c-b9b182aabf12/dqc_reference/reference_markers.fasta -out GCA_028680655.1_ASM2868065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:08:21,245] [INFO] Task succeeded: Blastn
[2023-06-17 11:08:21,249] [INFO] Selected 30 target genomes.
[2023-06-17 11:08:21,250] [INFO] Target genome list was writen to GCA_028680655.1_ASM2868065v1_genomic.fna/target_genomes.txt
[2023-06-17 11:08:21,260] [INFO] Task started: fastANI
[2023-06-17 11:08:21,261] [INFO] Running command: fastANI --query /var/lib/cwl/stgd31f4e09-c26c-4399-968d-b6870f5519f8/GCA_028680655.1_ASM2868065v1_genomic.fna.gz --refList GCA_028680655.1_ASM2868065v1_genomic.fna/target_genomes.txt --output GCA_028680655.1_ASM2868065v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:08:33,546] [INFO] Task succeeded: fastANI
[2023-06-17 11:08:33,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbb29c8e-20b4-4909-9f5c-b9b182aabf12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:08:33,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbb29c8e-20b4-4909-9f5c-b9b182aabf12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:08:33,548] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:08:33,549] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 11:08:33,549] [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
--------------------------------------------------------------------------------
[2023-06-17 11:08:33,551] [INFO] DFAST Taxonomy check result was written to GCA_028680655.1_ASM2868065v1_genomic.fna/tc_result.tsv
[2023-06-17 11:08:33,552] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:08:33,552] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:08:33,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbb29c8e-20b4-4909-9f5c-b9b182aabf12/dqc_reference/checkm_data
[2023-06-17 11:08:33,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:08:33,573] [INFO] Task started: CheckM
[2023-06-17 11:08:33,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028680655.1_ASM2868065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028680655.1_ASM2868065v1_genomic.fna/checkm_input GCA_028680655.1_ASM2868065v1_genomic.fna/checkm_result
[2023-06-17 11:08:46,657] [INFO] Task succeeded: CheckM
[2023-06-17 11:08:46,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 11:08:46,684] [INFO] ===== Completeness check finished =====
[2023-06-17 11:08:46,685] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:08:46,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028680655.1_ASM2868065v1_genomic.fna/markers.fasta)
[2023-06-17 11:08:46,686] [INFO] Task started: Blastn
[2023-06-17 11:08:46,686] [INFO] Running command: blastn -query GCA_028680655.1_ASM2868065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbb29c8e-20b4-4909-9f5c-b9b182aabf12/dqc_reference/reference_markers_gtdb.fasta -out GCA_028680655.1_ASM2868065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:08:47,554] [INFO] Task succeeded: Blastn
[2023-06-17 11:08:47,560] [INFO] Selected 25 target genomes.
[2023-06-17 11:08:47,560] [INFO] Target genome list was writen to GCA_028680655.1_ASM2868065v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:08:47,585] [INFO] Task started: fastANI
[2023-06-17 11:08:47,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgd31f4e09-c26c-4399-968d-b6870f5519f8/GCA_028680655.1_ASM2868065v1_genomic.fna.gz --refList GCA_028680655.1_ASM2868065v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028680655.1_ASM2868065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:08:52,785] [INFO] Task succeeded: fastANI
[2023-06-17 11:08:52,797] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 11:08:52,797] [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_012838395.1	s__DUPI01 sp012838395	80.7298	151	286	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__DUPI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521575.1	s__DUPI01 sp012521575	77.7945	122	286	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__DUPI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905206805.1	s__CAJLIR01 sp905206805	77.3808	51	286	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAJLIR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550255.1	s__UBA5026 sp900550255	76.5902	51	286	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.55	98.27	0.87	0.84	3	-
GCA_017887425.1	s__Faecisoma sp017887425	76.4512	54	286	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059545.1	s__UBA5026 sp015059545	76.2219	52	286	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:08:52,801] [INFO] GTDB search result was written to GCA_028680655.1_ASM2868065v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:08:52,801] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:08:52,805] [INFO] DFAST_QC result json was written to GCA_028680655.1_ASM2868065v1_genomic.fna/dqc_result.json
[2023-06-17 11:08:52,805] [INFO] DFAST_QC completed!
[2023-06-17 11:08:52,806] [INFO] Total running time: 0h0m35s