[2023-06-28 12:01:24,179] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:01:24,182] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:01:24,182] [INFO] DQC Reference Directory: /var/lib/cwl/stg266a48f6-a4c6-4183-bb33-255c4102667b/dqc_reference
[2023-06-28 12:01:25,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:01:25,424] [INFO] Task started: Prodigal
[2023-06-28 12:01:25,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg43d60b78-4fab-4e74-9e62-0663e946f72d/GCA_015264975.1_ASM1526497v1_genomic.fna.gz | prodigal -d GCA_015264975.1_ASM1526497v1_genomic.fna/cds.fna -a GCA_015264975.1_ASM1526497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:01:28,354] [INFO] Task succeeded: Prodigal
[2023-06-28 12:01:28,354] [INFO] Task started: HMMsearch
[2023-06-28 12:01:28,354] [INFO] Running command: hmmsearch --tblout GCA_015264975.1_ASM1526497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg266a48f6-a4c6-4183-bb33-255c4102667b/dqc_reference/reference_markers.hmm GCA_015264975.1_ASM1526497v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:01:28,587] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:01:28,588] [INFO] Found 6/6 markers.
[2023-06-28 12:01:28,614] [INFO] Query marker FASTA was written to GCA_015264975.1_ASM1526497v1_genomic.fna/markers.fasta
[2023-06-28 12:01:28,614] [INFO] Task started: Blastn
[2023-06-28 12:01:28,614] [INFO] Running command: blastn -query GCA_015264975.1_ASM1526497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg266a48f6-a4c6-4183-bb33-255c4102667b/dqc_reference/reference_markers.fasta -out GCA_015264975.1_ASM1526497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:29,309] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:29,312] [INFO] Selected 18 target genomes.
[2023-06-28 12:01:29,313] [INFO] Target genome list was writen to GCA_015264975.1_ASM1526497v1_genomic.fna/target_genomes.txt
[2023-06-28 12:01:29,354] [INFO] Task started: fastANI
[2023-06-28 12:01:29,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg43d60b78-4fab-4e74-9e62-0663e946f72d/GCA_015264975.1_ASM1526497v1_genomic.fna.gz --refList GCA_015264975.1_ASM1526497v1_genomic.fna/target_genomes.txt --output GCA_015264975.1_ASM1526497v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:01:36,775] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:36,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg266a48f6-a4c6-4183-bb33-255c4102667b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:01:36,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg266a48f6-a4c6-4183-bb33-255c4102667b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:01:36,781] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:01:36,782] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:01:36,782] [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
Granulicatella adiacens	strain=ATCC 49175	GCA_025150565.1	46124	46124	type	True	88.5722	349	416	95	below_threshold
Granulicatella adiacens	strain=ATCC 49175	GCA_000160675.1	46124	46124	type	True	88.5542	346	416	95	below_threshold
Granulicatella adiacens	strain=FDAARGOS_1477	GCA_019931005.1	46124	46124	type	True	88.4819	352	416	95	below_threshold
Granulicatella balaenopterae	strain=DSM 15827	GCA_900111135.1	137733	137733	type	True	78.8187	76	416	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:01:36,784] [INFO] DFAST Taxonomy check result was written to GCA_015264975.1_ASM1526497v1_genomic.fna/tc_result.tsv
[2023-06-28 12:01:36,785] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:01:36,785] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:01:36,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg266a48f6-a4c6-4183-bb33-255c4102667b/dqc_reference/checkm_data
[2023-06-28 12:01:36,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:01:36,808] [INFO] Task started: CheckM
[2023-06-28 12:01:36,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015264975.1_ASM1526497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015264975.1_ASM1526497v1_genomic.fna/checkm_input GCA_015264975.1_ASM1526497v1_genomic.fna/checkm_result
[2023-06-28 12:01:55,118] [INFO] Task succeeded: CheckM
[2023-06-28 12:01:55,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 15.03%
Strain heterogeneity: 21.43%
--------------------------------------------------------------------------------
[2023-06-28 12:01:55,143] [INFO] ===== Completeness check finished =====
[2023-06-28 12:01:55,143] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:01:55,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015264975.1_ASM1526497v1_genomic.fna/markers.fasta)
[2023-06-28 12:01:55,144] [INFO] Task started: Blastn
[2023-06-28 12:01:55,144] [INFO] Running command: blastn -query GCA_015264975.1_ASM1526497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg266a48f6-a4c6-4183-bb33-255c4102667b/dqc_reference/reference_markers_gtdb.fasta -out GCA_015264975.1_ASM1526497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:56,148] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:56,152] [INFO] Selected 7 target genomes.
[2023-06-28 12:01:56,153] [INFO] Target genome list was writen to GCA_015264975.1_ASM1526497v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:01:56,160] [INFO] Task started: fastANI
[2023-06-28 12:01:56,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg43d60b78-4fab-4e74-9e62-0663e946f72d/GCA_015264975.1_ASM1526497v1_genomic.fna.gz --refList GCA_015264975.1_ASM1526497v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015264975.1_ASM1526497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:01:58,525] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:58,533] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 12:01:58,533] [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_001058355.1	s__Granulicatella sp001058355	95.6659	293	416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	95.40	95.27	0.77	0.71	6	inconclusive
GCF_001071995.1	s__Granulicatella sp001071995	95.0755	380	416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_018364485.1	s__Granulicatella adiacens_A	94.8278	338	416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015264885.1	s__Granulicatella sp015264885	94.596	254	416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	95.15	95.15	0.88	0.88	2	-
GCA_900551535.1	s__Granulicatella sp900551535	94.5476	289	416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000160675.1	s__Granulicatella adiacens	88.5762	345	416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	96.49	96.38	0.91	0.88	11	-
GCA_905371865.1	s__Granulicatella sp905371865	87.8145	234	416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:01:58,539] [INFO] GTDB search result was written to GCA_015264975.1_ASM1526497v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:01:58,540] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:01:58,548] [INFO] DFAST_QC result json was written to GCA_015264975.1_ASM1526497v1_genomic.fna/dqc_result.json
[2023-06-28 12:01:58,549] [INFO] DFAST_QC completed!
[2023-06-28 12:01:58,549] [INFO] Total running time: 0h0m34s