[2023-06-17 04:19:21,689] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:19:21,692] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:19:21,692] [INFO] DQC Reference Directory: /var/lib/cwl/stgaedfc13e-bdbe-4f4c-8716-147bfe9721cf/dqc_reference
[2023-06-17 04:19:22,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:19:23,000] [INFO] Task started: Prodigal
[2023-06-17 04:19:23,000] [INFO] Running command: gunzip -c /var/lib/cwl/stg917ebcd4-04de-426a-b78a-273d9e9b1941/GCA_028708985.1_ASM2870898v1_genomic.fna.gz | prodigal -d GCA_028708985.1_ASM2870898v1_genomic.fna/cds.fna -a GCA_028708985.1_ASM2870898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:19:44,606] [INFO] Task succeeded: Prodigal
[2023-06-17 04:19:44,606] [INFO] Task started: HMMsearch
[2023-06-17 04:19:44,607] [INFO] Running command: hmmsearch --tblout GCA_028708985.1_ASM2870898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaedfc13e-bdbe-4f4c-8716-147bfe9721cf/dqc_reference/reference_markers.hmm GCA_028708985.1_ASM2870898v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:19:44,879] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:19:44,880] [INFO] Found 6/6 markers.
[2023-06-17 04:19:44,914] [INFO] Query marker FASTA was written to GCA_028708985.1_ASM2870898v1_genomic.fna/markers.fasta
[2023-06-17 04:19:44,915] [INFO] Task started: Blastn
[2023-06-17 04:19:44,915] [INFO] Running command: blastn -query GCA_028708985.1_ASM2870898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaedfc13e-bdbe-4f4c-8716-147bfe9721cf/dqc_reference/reference_markers.fasta -out GCA_028708985.1_ASM2870898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:19:45,573] [INFO] Task succeeded: Blastn
[2023-06-17 04:19:45,577] [INFO] Selected 30 target genomes.
[2023-06-17 04:19:45,578] [INFO] Target genome list was writen to GCA_028708985.1_ASM2870898v1_genomic.fna/target_genomes.txt
[2023-06-17 04:19:45,582] [INFO] Task started: fastANI
[2023-06-17 04:19:45,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg917ebcd4-04de-426a-b78a-273d9e9b1941/GCA_028708985.1_ASM2870898v1_genomic.fna.gz --refList GCA_028708985.1_ASM2870898v1_genomic.fna/target_genomes.txt --output GCA_028708985.1_ASM2870898v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:20:08,117] [INFO] Task succeeded: fastANI
[2023-06-17 04:20:08,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaedfc13e-bdbe-4f4c-8716-147bfe9721cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:20:08,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaedfc13e-bdbe-4f4c-8716-147bfe9721cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:20:08,119] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 04:20:08,119] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 04:20:08,119] [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 04:20:08,121] [INFO] DFAST Taxonomy check result was written to GCA_028708985.1_ASM2870898v1_genomic.fna/tc_result.tsv
[2023-06-17 04:20:08,122] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:20:08,122] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:20:08,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaedfc13e-bdbe-4f4c-8716-147bfe9721cf/dqc_reference/checkm_data
[2023-06-17 04:20:08,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:20:08,167] [INFO] Task started: CheckM
[2023-06-17 04:20:08,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708985.1_ASM2870898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708985.1_ASM2870898v1_genomic.fna/checkm_input GCA_028708985.1_ASM2870898v1_genomic.fna/checkm_result
[2023-06-17 04:21:07,418] [INFO] Task succeeded: CheckM
[2023-06-17 04:21:07,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 04:21:07,444] [INFO] ===== Completeness check finished =====
[2023-06-17 04:21:07,444] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:21:07,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708985.1_ASM2870898v1_genomic.fna/markers.fasta)
[2023-06-17 04:21:07,445] [INFO] Task started: Blastn
[2023-06-17 04:21:07,445] [INFO] Running command: blastn -query GCA_028708985.1_ASM2870898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaedfc13e-bdbe-4f4c-8716-147bfe9721cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708985.1_ASM2870898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:21:08,218] [INFO] Task succeeded: Blastn
[2023-06-17 04:21:08,224] [INFO] Selected 20 target genomes.
[2023-06-17 04:21:08,224] [INFO] Target genome list was writen to GCA_028708985.1_ASM2870898v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:21:08,234] [INFO] Task started: fastANI
[2023-06-17 04:21:08,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg917ebcd4-04de-426a-b78a-273d9e9b1941/GCA_028708985.1_ASM2870898v1_genomic.fna.gz --refList GCA_028708985.1_ASM2870898v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708985.1_ASM2870898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:21:19,171] [INFO] Task succeeded: fastANI
[2023-06-17 04:21:19,182] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 04:21:19,182] [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_012523265.1	s__SABY01 sp012523265	98.8642	942	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4484-276;g__SABY01	95.0	98.83	98.83	0.81	0.81	2	conclusive
GCA_009928785.1	s__SABY01 sp009928785	84.6938	919	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4484-276;g__SABY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018400545.1	s__SABY01 sp018400545	76.0344	56	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4484-276;g__SABY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860585.1	s__RZYY01 sp014860585	75.819	59	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4484-276;g__RZYY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 04:21:19,184] [INFO] GTDB search result was written to GCA_028708985.1_ASM2870898v1_genomic.fna/result_gtdb.tsv
[2023-06-17 04:21:19,185] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:21:19,188] [INFO] DFAST_QC result json was written to GCA_028708985.1_ASM2870898v1_genomic.fna/dqc_result.json
[2023-06-17 04:21:19,188] [INFO] DFAST_QC completed!
[2023-06-17 04:21:19,188] [INFO] Total running time: 0h1m57s