[2023-06-17 16:36:38,898] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:36:38,901] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:36:38,902] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa70f322-ee5f-4a47-8698-575a14647ca8/dqc_reference
[2023-06-17 16:36:40,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:36:40,102] [INFO] Task started: Prodigal
[2023-06-17 16:36:40,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg03d9c3cc-4971-4805-ba2a-6bcbfffac18a/GCA_009927355.1_ASM992735v1_genomic.fna.gz | prodigal -d GCA_009927355.1_ASM992735v1_genomic.fna/cds.fna -a GCA_009927355.1_ASM992735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:36:44,606] [INFO] Task succeeded: Prodigal
[2023-06-17 16:36:44,606] [INFO] Task started: HMMsearch
[2023-06-17 16:36:44,606] [INFO] Running command: hmmsearch --tblout GCA_009927355.1_ASM992735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa70f322-ee5f-4a47-8698-575a14647ca8/dqc_reference/reference_markers.hmm GCA_009927355.1_ASM992735v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:36:44,795] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:36:44,796] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg03d9c3cc-4971-4805-ba2a-6bcbfffac18a/GCA_009927355.1_ASM992735v1_genomic.fna.gz]
[2023-06-17 16:36:44,821] [INFO] Query marker FASTA was written to GCA_009927355.1_ASM992735v1_genomic.fna/markers.fasta
[2023-06-17 16:36:44,821] [INFO] Task started: Blastn
[2023-06-17 16:36:44,821] [INFO] Running command: blastn -query GCA_009927355.1_ASM992735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa70f322-ee5f-4a47-8698-575a14647ca8/dqc_reference/reference_markers.fasta -out GCA_009927355.1_ASM992735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:36:45,382] [INFO] Task succeeded: Blastn
[2023-06-17 16:36:45,386] [INFO] Selected 21 target genomes.
[2023-06-17 16:36:45,387] [INFO] Target genome list was writen to GCA_009927355.1_ASM992735v1_genomic.fna/target_genomes.txt
[2023-06-17 16:36:45,390] [INFO] Task started: fastANI
[2023-06-17 16:36:45,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg03d9c3cc-4971-4805-ba2a-6bcbfffac18a/GCA_009927355.1_ASM992735v1_genomic.fna.gz --refList GCA_009927355.1_ASM992735v1_genomic.fna/target_genomes.txt --output GCA_009927355.1_ASM992735v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:36:56,780] [INFO] Task succeeded: fastANI
[2023-06-17 16:36:56,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa70f322-ee5f-4a47-8698-575a14647ca8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:36:56,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa70f322-ee5f-4a47-8698-575a14647ca8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:36:56,783] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:36:56,783] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 16:36:56,783] [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 16:36:56,785] [INFO] DFAST Taxonomy check result was written to GCA_009927355.1_ASM992735v1_genomic.fna/tc_result.tsv
[2023-06-17 16:36:56,785] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:36:56,786] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:36:56,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa70f322-ee5f-4a47-8698-575a14647ca8/dqc_reference/checkm_data
[2023-06-17 16:36:56,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:36:56,816] [INFO] Task started: CheckM
[2023-06-17 16:36:56,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009927355.1_ASM992735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009927355.1_ASM992735v1_genomic.fna/checkm_input GCA_009927355.1_ASM992735v1_genomic.fna/checkm_result
[2023-06-17 16:37:16,660] [INFO] Task succeeded: CheckM
[2023-06-17 16:37:16,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:37:16,682] [INFO] ===== Completeness check finished =====
[2023-06-17 16:37:16,682] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:37:16,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009927355.1_ASM992735v1_genomic.fna/markers.fasta)
[2023-06-17 16:37:16,682] [INFO] Task started: Blastn
[2023-06-17 16:37:16,682] [INFO] Running command: blastn -query GCA_009927355.1_ASM992735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa70f322-ee5f-4a47-8698-575a14647ca8/dqc_reference/reference_markers_gtdb.fasta -out GCA_009927355.1_ASM992735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:37:17,450] [INFO] Task succeeded: Blastn
[2023-06-17 16:37:17,454] [INFO] Selected 14 target genomes.
[2023-06-17 16:37:17,454] [INFO] Target genome list was writen to GCA_009927355.1_ASM992735v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:37:17,465] [INFO] Task started: fastANI
[2023-06-17 16:37:17,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg03d9c3cc-4971-4805-ba2a-6bcbfffac18a/GCA_009927355.1_ASM992735v1_genomic.fna.gz --refList GCA_009927355.1_ASM992735v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009927355.1_ASM992735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:37:23,996] [INFO] Task succeeded: fastANI
[2023-06-17 16:37:24,002] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:37:24,002] [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_002342225.1	s__UBA2466 sp002342225	98.8435	565	640	d__Bacteria;p__Bdellovibrionota;c__FAC87;o__UBA2466;f__UBA2466;g__UBA2466	95.0	99.36	98.92	0.89	0.88	4	conclusive
GCA_005776395.1	s__UBA2466 sp005776395	77.7892	156	640	d__Bacteria;p__Bdellovibrionota;c__FAC87;o__UBA2466;f__UBA2466;g__UBA2466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299195.1	s__UBA2466 sp900299195	77.7541	130	640	d__Bacteria;p__Bdellovibrionota;c__FAC87;o__UBA2466;f__UBA2466;g__UBA2466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875135.1	s__UBA2466 sp016875135	77.3623	116	640	d__Bacteria;p__Bdellovibrionota;c__FAC87;o__UBA2466;f__UBA2466;g__UBA2466	95.0	97.94	97.94	0.85	0.85	2	-
GCA_013205415.1	s__UBA2466 sp013205415	76.8493	59	640	d__Bacteria;p__Bdellovibrionota;c__FAC87;o__UBA2466;f__UBA2466;g__UBA2466	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 16:37:24,004] [INFO] GTDB search result was written to GCA_009927355.1_ASM992735v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:37:24,005] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:37:24,008] [INFO] DFAST_QC result json was written to GCA_009927355.1_ASM992735v1_genomic.fna/dqc_result.json
[2023-06-17 16:37:24,008] [INFO] DFAST_QC completed!
[2023-06-17 16:37:24,008] [INFO] Total running time: 0h0m45s