[2023-06-17 06:45:08,908] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:45:08,912] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:45:08,913] [INFO] DQC Reference Directory: /var/lib/cwl/stg10461c37-3361-41ed-a908-8c954f3db942/dqc_reference
[2023-06-17 06:45:10,224] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:45:10,225] [INFO] Task started: Prodigal
[2023-06-17 06:45:10,225] [INFO] Running command: gunzip -c /var/lib/cwl/stg311bfef3-cba5-46f9-99ef-8f652b8a95f5/GCA_028708285.1_ASM2870828v1_genomic.fna.gz | prodigal -d GCA_028708285.1_ASM2870828v1_genomic.fna/cds.fna -a GCA_028708285.1_ASM2870828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:45:11,739] [INFO] Task succeeded: Prodigal
[2023-06-17 06:45:11,740] [INFO] Task started: HMMsearch
[2023-06-17 06:45:11,740] [INFO] Running command: hmmsearch --tblout GCA_028708285.1_ASM2870828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10461c37-3361-41ed-a908-8c954f3db942/dqc_reference/reference_markers.hmm GCA_028708285.1_ASM2870828v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:45:12,063] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:45:12,065] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg311bfef3-cba5-46f9-99ef-8f652b8a95f5/GCA_028708285.1_ASM2870828v1_genomic.fna.gz]
[2023-06-17 06:45:12,080] [INFO] Query marker FASTA was written to GCA_028708285.1_ASM2870828v1_genomic.fna/markers.fasta
[2023-06-17 06:45:12,081] [INFO] Task started: Blastn
[2023-06-17 06:45:12,081] [INFO] Running command: blastn -query GCA_028708285.1_ASM2870828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10461c37-3361-41ed-a908-8c954f3db942/dqc_reference/reference_markers.fasta -out GCA_028708285.1_ASM2870828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:45:14,569] [INFO] Task succeeded: Blastn
[2023-06-17 06:45:14,574] [INFO] Selected 30 target genomes.
[2023-06-17 06:45:14,575] [INFO] Target genome list was writen to GCA_028708285.1_ASM2870828v1_genomic.fna/target_genomes.txt
[2023-06-17 06:45:14,581] [INFO] Task started: fastANI
[2023-06-17 06:45:14,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg311bfef3-cba5-46f9-99ef-8f652b8a95f5/GCA_028708285.1_ASM2870828v1_genomic.fna.gz --refList GCA_028708285.1_ASM2870828v1_genomic.fna/target_genomes.txt --output GCA_028708285.1_ASM2870828v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:45:26,956] [INFO] Task succeeded: fastANI
[2023-06-17 06:45:26,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10461c37-3361-41ed-a908-8c954f3db942/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:45:26,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10461c37-3361-41ed-a908-8c954f3db942/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:45:26,960] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:45:26,960] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 06:45:26,960] [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 06:45:26,963] [INFO] DFAST Taxonomy check result was written to GCA_028708285.1_ASM2870828v1_genomic.fna/tc_result.tsv
[2023-06-17 06:45:26,963] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:45:26,964] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:45:26,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10461c37-3361-41ed-a908-8c954f3db942/dqc_reference/checkm_data
[2023-06-17 06:45:26,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:45:26,986] [INFO] Task started: CheckM
[2023-06-17 06:45:26,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708285.1_ASM2870828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708285.1_ASM2870828v1_genomic.fna/checkm_input GCA_028708285.1_ASM2870828v1_genomic.fna/checkm_result
[2023-06-17 06:45:40,404] [INFO] Task succeeded: CheckM
[2023-06-17 06:45:40,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:45:40,422] [INFO] ===== Completeness check finished =====
[2023-06-17 06:45:40,422] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:45:40,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708285.1_ASM2870828v1_genomic.fna/markers.fasta)
[2023-06-17 06:45:40,423] [INFO] Task started: Blastn
[2023-06-17 06:45:40,423] [INFO] Running command: blastn -query GCA_028708285.1_ASM2870828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10461c37-3361-41ed-a908-8c954f3db942/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708285.1_ASM2870828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:45:41,217] [INFO] Task succeeded: Blastn
[2023-06-17 06:45:41,223] [INFO] Selected 24 target genomes.
[2023-06-17 06:45:41,223] [INFO] Target genome list was writen to GCA_028708285.1_ASM2870828v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:45:41,231] [INFO] Task started: fastANI
[2023-06-17 06:45:41,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg311bfef3-cba5-46f9-99ef-8f652b8a95f5/GCA_028708285.1_ASM2870828v1_genomic.fna.gz --refList GCA_028708285.1_ASM2870828v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708285.1_ASM2870828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:45:46,020] [INFO] Task succeeded: fastANI
[2023-06-17 06:45:46,028] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 06:45:46,028] [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	80.7685	166	327	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	77.8246	130	327	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__DUPI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546275.1	s__UMGS872 sp900546275	77.1852	50	327	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS872	95.0	97.38	97.34	0.83	0.82	3	-
GCA_012520435.1	s__JAAYOI01 sp012520435	77.1464	90	327	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__JAAYOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059545.1	s__UBA5026 sp015059545	76.7995	51	327	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550255.1	s__UBA5026 sp900550255	76.627	57	327	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	76.4462	66	327	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 06:45:46,030] [INFO] GTDB search result was written to GCA_028708285.1_ASM2870828v1_genomic.fna/result_gtdb.tsv
[2023-06-17 06:45:46,031] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:45:46,034] [INFO] DFAST_QC result json was written to GCA_028708285.1_ASM2870828v1_genomic.fna/dqc_result.json
[2023-06-17 06:45:46,034] [INFO] DFAST_QC completed!
[2023-06-17 06:45:46,034] [INFO] Total running time: 0h0m37s