[2023-06-16 21:17:18,615] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:17:18,622] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:17:18,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c23e859-610d-4686-8211-ae64dcbd8177/dqc_reference
[2023-06-16 21:17:20,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:17:20,031] [INFO] Task started: Prodigal
[2023-06-16 21:17:20,031] [INFO] Running command: gunzip -c /var/lib/cwl/stg48dc21eb-7a99-4ec0-819a-ec865c88bdff/GCA_028685595.1_ASM2868559v1_genomic.fna.gz | prodigal -d GCA_028685595.1_ASM2868559v1_genomic.fna/cds.fna -a GCA_028685595.1_ASM2868559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:17:22,367] [INFO] Task succeeded: Prodigal
[2023-06-16 21:17:22,367] [INFO] Task started: HMMsearch
[2023-06-16 21:17:22,367] [INFO] Running command: hmmsearch --tblout GCA_028685595.1_ASM2868559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c23e859-610d-4686-8211-ae64dcbd8177/dqc_reference/reference_markers.hmm GCA_028685595.1_ASM2868559v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:17:22,634] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:17:22,636] [INFO] Found 6/6 markers.
[2023-06-16 21:17:22,659] [INFO] Query marker FASTA was written to GCA_028685595.1_ASM2868559v1_genomic.fna/markers.fasta
[2023-06-16 21:17:22,660] [INFO] Task started: Blastn
[2023-06-16 21:17:22,660] [INFO] Running command: blastn -query GCA_028685595.1_ASM2868559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c23e859-610d-4686-8211-ae64dcbd8177/dqc_reference/reference_markers.fasta -out GCA_028685595.1_ASM2868559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:17:23,720] [INFO] Task succeeded: Blastn
[2023-06-16 21:17:23,724] [INFO] Selected 14 target genomes.
[2023-06-16 21:17:23,725] [INFO] Target genome list was writen to GCA_028685595.1_ASM2868559v1_genomic.fna/target_genomes.txt
[2023-06-16 21:17:23,726] [INFO] Task started: fastANI
[2023-06-16 21:17:23,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg48dc21eb-7a99-4ec0-819a-ec865c88bdff/GCA_028685595.1_ASM2868559v1_genomic.fna.gz --refList GCA_028685595.1_ASM2868559v1_genomic.fna/target_genomes.txt --output GCA_028685595.1_ASM2868559v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:17:30,889] [INFO] Task succeeded: fastANI
[2023-06-16 21:17:30,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c23e859-610d-4686-8211-ae64dcbd8177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:17:30,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c23e859-610d-4686-8211-ae64dcbd8177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:17:30,892] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 21:17:30,892] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 21:17:30,892] [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
--------------------------------------------------------------------------------
[2023-06-16 21:17:30,894] [INFO] DFAST Taxonomy check result was written to GCA_028685595.1_ASM2868559v1_genomic.fna/tc_result.tsv
[2023-06-16 21:17:30,895] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:17:30,895] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:17:30,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c23e859-610d-4686-8211-ae64dcbd8177/dqc_reference/checkm_data
[2023-06-16 21:17:30,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:17:30,931] [INFO] Task started: CheckM
[2023-06-16 21:17:30,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028685595.1_ASM2868559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028685595.1_ASM2868559v1_genomic.fna/checkm_input GCA_028685595.1_ASM2868559v1_genomic.fna/checkm_result
[2023-06-16 21:17:47,414] [INFO] Task succeeded: CheckM
[2023-06-16 21:17:47,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:17:47,439] [INFO] ===== Completeness check finished =====
[2023-06-16 21:17:47,440] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:17:47,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028685595.1_ASM2868559v1_genomic.fna/markers.fasta)
[2023-06-16 21:17:47,441] [INFO] Task started: Blastn
[2023-06-16 21:17:47,441] [INFO] Running command: blastn -query GCA_028685595.1_ASM2868559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c23e859-610d-4686-8211-ae64dcbd8177/dqc_reference/reference_markers_gtdb.fasta -out GCA_028685595.1_ASM2868559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:17:48,278] [INFO] Task succeeded: Blastn
[2023-06-16 21:17:48,283] [INFO] Selected 17 target genomes.
[2023-06-16 21:17:48,283] [INFO] Target genome list was writen to GCA_028685595.1_ASM2868559v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:17:48,288] [INFO] Task started: fastANI
[2023-06-16 21:17:48,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg48dc21eb-7a99-4ec0-819a-ec865c88bdff/GCA_028685595.1_ASM2868559v1_genomic.fna.gz --refList GCA_028685595.1_ASM2868559v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028685595.1_ASM2868559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:17:53,903] [INFO] Task succeeded: fastANI
[2023-06-16 21:17:53,915] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 21:17:53,916] [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_018433585.1	s__JAHDQW01 sp018433585	79.8175	269	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__JAHDQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761395.1	s__RUG658 sp902761395	77.3621	82	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__RUG658	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017525905.1	s__RUG658 sp017525905	77.2949	100	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__RUG658	95.0	97.07	97.07	0.86	0.86	2	-
GCA_017528425.1	s__RUG658 sp017528425	77.132	105	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__RUG658	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321055.1	s__RUG658 sp900321055	77.1214	94	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__RUG658	95.0	99.63	99.63	0.99	0.99	2	-
GCA_017529005.1	s__RUG658 sp017529005	77.0982	122	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__RUG658	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651625.1	s__RUG658 sp017651625	77.0226	106	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__RUG658	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002448285.1	s__RUG658 sp002448285	76.8605	116	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__RUG658	95.0	99.20	99.10	0.95	0.93	8	-
GCA_018433245.1	s__JAHDRN01 sp018433245	76.8563	91	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__JAHDRN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316875.1	s__RUG240 sp900316875	76.5538	80	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__RUG240	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017413305.1	s__RUG658 sp017413305	76.5271	55	411	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__RUG658	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 21:17:53,919] [INFO] GTDB search result was written to GCA_028685595.1_ASM2868559v1_genomic.fna/result_gtdb.tsv
[2023-06-16 21:17:53,919] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:17:53,923] [INFO] DFAST_QC result json was written to GCA_028685595.1_ASM2868559v1_genomic.fna/dqc_result.json
[2023-06-16 21:17:53,923] [INFO] DFAST_QC completed!
[2023-06-16 21:17:53,923] [INFO] Total running time: 0h0m35s