[2023-06-17 06:00:24,251] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:00:24,270] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:00:24,270] [INFO] DQC Reference Directory: /var/lib/cwl/stga03213fa-4811-49e0-8b27-18f885f95083/dqc_reference
[2023-06-17 06:00:25,570] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:00:25,571] [INFO] Task started: Prodigal
[2023-06-17 06:00:25,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f099492-db35-4588-8e16-7ae1de215c56/GCA_028875335.1_ASM2887533v1_genomic.fna.gz | prodigal -d GCA_028875335.1_ASM2887533v1_genomic.fna/cds.fna -a GCA_028875335.1_ASM2887533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:00:41,873] [INFO] Task succeeded: Prodigal
[2023-06-17 06:00:41,874] [INFO] Task started: HMMsearch
[2023-06-17 06:00:41,874] [INFO] Running command: hmmsearch --tblout GCA_028875335.1_ASM2887533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga03213fa-4811-49e0-8b27-18f885f95083/dqc_reference/reference_markers.hmm GCA_028875335.1_ASM2887533v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:00:42,208] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:00:42,209] [INFO] Found 6/6 markers.
[2023-06-17 06:00:42,261] [INFO] Query marker FASTA was written to GCA_028875335.1_ASM2887533v1_genomic.fna/markers.fasta
[2023-06-17 06:00:42,262] [INFO] Task started: Blastn
[2023-06-17 06:00:42,262] [INFO] Running command: blastn -query GCA_028875335.1_ASM2887533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga03213fa-4811-49e0-8b27-18f885f95083/dqc_reference/reference_markers.fasta -out GCA_028875335.1_ASM2887533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:00:42,902] [INFO] Task succeeded: Blastn
[2023-06-17 06:00:42,908] [INFO] Selected 45 target genomes.
[2023-06-17 06:00:42,909] [INFO] Target genome list was writen to GCA_028875335.1_ASM2887533v1_genomic.fna/target_genomes.txt
[2023-06-17 06:00:42,922] [INFO] Task started: fastANI
[2023-06-17 06:00:42,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f099492-db35-4588-8e16-7ae1de215c56/GCA_028875335.1_ASM2887533v1_genomic.fna.gz --refList GCA_028875335.1_ASM2887533v1_genomic.fna/target_genomes.txt --output GCA_028875335.1_ASM2887533v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:01:13,050] [INFO] Task succeeded: fastANI
[2023-06-17 06:01:13,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga03213fa-4811-49e0-8b27-18f885f95083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:01:13,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga03213fa-4811-49e0-8b27-18f885f95083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:01:13,052] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:01:13,052] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 06:01:13,052] [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 06:01:13,054] [INFO] DFAST Taxonomy check result was written to GCA_028875335.1_ASM2887533v1_genomic.fna/tc_result.tsv
[2023-06-17 06:01:13,055] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:01:13,055] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:01:13,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga03213fa-4811-49e0-8b27-18f885f95083/dqc_reference/checkm_data
[2023-06-17 06:01:13,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:01:13,116] [INFO] Task started: CheckM
[2023-06-17 06:01:13,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028875335.1_ASM2887533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028875335.1_ASM2887533v1_genomic.fna/checkm_input GCA_028875335.1_ASM2887533v1_genomic.fna/checkm_result
[2023-06-17 06:02:01,243] [INFO] Task succeeded: CheckM
[2023-06-17 06:02:01,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:02:01,271] [INFO] ===== Completeness check finished =====
[2023-06-17 06:02:01,271] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:02:01,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028875335.1_ASM2887533v1_genomic.fna/markers.fasta)
[2023-06-17 06:02:01,272] [INFO] Task started: Blastn
[2023-06-17 06:02:01,272] [INFO] Running command: blastn -query GCA_028875335.1_ASM2887533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga03213fa-4811-49e0-8b27-18f885f95083/dqc_reference/reference_markers_gtdb.fasta -out GCA_028875335.1_ASM2887533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:02:02,145] [INFO] Task succeeded: Blastn
[2023-06-17 06:02:02,151] [INFO] Selected 14 target genomes.
[2023-06-17 06:02:02,151] [INFO] Target genome list was writen to GCA_028875335.1_ASM2887533v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:02:02,165] [INFO] Task started: fastANI
[2023-06-17 06:02:02,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f099492-db35-4588-8e16-7ae1de215c56/GCA_028875335.1_ASM2887533v1_genomic.fna.gz --refList GCA_028875335.1_ASM2887533v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028875335.1_ASM2887533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:02:15,841] [INFO] Task succeeded: fastANI
[2023-06-17 06:02:15,854] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 06:02:15,854] [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_009841115.1	s__GCA-2724215 sp009841115	91.3986	1369	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.89	99.89	0.98	0.96	3	-
GCA_009840005.1	s__GCA-2724215 sp009840005	91.0499	1431	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.94	99.94	0.99	0.99	2	-
GCA_009845645.1	s__GCA-2724215 sp009845645	90.8432	838	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571365.1	s__GCA-2724215 sp007571365	86.8382	1142	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724215.1	s__GCA-2724215 sp002724215	77.4479	390	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660315.1	s__GCA-2724215 sp015660315	77.0134	230	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018672475.1	s__GCA-2724215 sp018672475	77.0021	301	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.78	99.75	0.95	0.94	9	-
GCA_016187725.1	s__SICG01 sp016187725	76.0471	109	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726335.1	s__UBA8231 sp002726335	75.4006	66	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893785.1	s__CAITNQ01 sp903893785	75.243	62	1783	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__CAITNQ01	95.0	99.57	99.57	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-17 06:02:15,856] [INFO] GTDB search result was written to GCA_028875335.1_ASM2887533v1_genomic.fna/result_gtdb.tsv
[2023-06-17 06:02:15,857] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:02:15,860] [INFO] DFAST_QC result json was written to GCA_028875335.1_ASM2887533v1_genomic.fna/dqc_result.json
[2023-06-17 06:02:15,861] [INFO] DFAST_QC completed!
[2023-06-17 06:02:15,861] [INFO] Total running time: 0h1m52s