[2023-06-16 19:11:15,185] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:11:15,188] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:11:15,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c948d04-d594-45df-bfa1-35e6526874fa/dqc_reference
[2023-06-16 19:11:16,500] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:11:16,501] [INFO] Task started: Prodigal
[2023-06-16 19:11:16,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg071cd1af-1f23-444c-9da7-9d0a6438b7b4/GCA_009779675.1_ASM977967v1_genomic.fna.gz | prodigal -d GCA_009779675.1_ASM977967v1_genomic.fna/cds.fna -a GCA_009779675.1_ASM977967v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:11:22,192] [INFO] Task succeeded: Prodigal
[2023-06-16 19:11:22,193] [INFO] Task started: HMMsearch
[2023-06-16 19:11:22,193] [INFO] Running command: hmmsearch --tblout GCA_009779675.1_ASM977967v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c948d04-d594-45df-bfa1-35e6526874fa/dqc_reference/reference_markers.hmm GCA_009779675.1_ASM977967v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:11:22,426] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:11:22,427] [INFO] Found 6/6 markers.
[2023-06-16 19:11:22,448] [INFO] Query marker FASTA was written to GCA_009779675.1_ASM977967v1_genomic.fna/markers.fasta
[2023-06-16 19:11:22,449] [INFO] Task started: Blastn
[2023-06-16 19:11:22,449] [INFO] Running command: blastn -query GCA_009779675.1_ASM977967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c948d04-d594-45df-bfa1-35e6526874fa/dqc_reference/reference_markers.fasta -out GCA_009779675.1_ASM977967v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:23,130] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:23,135] [INFO] Selected 28 target genomes.
[2023-06-16 19:11:23,135] [INFO] Target genome list was writen to GCA_009779675.1_ASM977967v1_genomic.fna/target_genomes.txt
[2023-06-16 19:11:23,142] [INFO] Task started: fastANI
[2023-06-16 19:11:23,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg071cd1af-1f23-444c-9da7-9d0a6438b7b4/GCA_009779675.1_ASM977967v1_genomic.fna.gz --refList GCA_009779675.1_ASM977967v1_genomic.fna/target_genomes.txt --output GCA_009779675.1_ASM977967v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:11:39,049] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:39,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c948d04-d594-45df-bfa1-35e6526874fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:11:39,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c948d04-d594-45df-bfa1-35e6526874fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:11:39,052] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:11:39,052] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:11:39,052] [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
--------------------------------------------------------------------------------
[2023-06-16 19:11:39,054] [INFO] DFAST Taxonomy check result was written to GCA_009779675.1_ASM977967v1_genomic.fna/tc_result.tsv
[2023-06-16 19:11:39,054] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:11:39,054] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:11:39,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c948d04-d594-45df-bfa1-35e6526874fa/dqc_reference/checkm_data
[2023-06-16 19:11:39,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:11:39,084] [INFO] Task started: CheckM
[2023-06-16 19:11:39,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009779675.1_ASM977967v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009779675.1_ASM977967v1_genomic.fna/checkm_input GCA_009779675.1_ASM977967v1_genomic.fna/checkm_result
[2023-06-16 19:12:02,023] [INFO] Task succeeded: CheckM
[2023-06-16 19:12:02,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:12:02,046] [INFO] ===== Completeness check finished =====
[2023-06-16 19:12:02,046] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:12:02,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009779675.1_ASM977967v1_genomic.fna/markers.fasta)
[2023-06-16 19:12:02,047] [INFO] Task started: Blastn
[2023-06-16 19:12:02,047] [INFO] Running command: blastn -query GCA_009779675.1_ASM977967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c948d04-d594-45df-bfa1-35e6526874fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_009779675.1_ASM977967v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:12:02,996] [INFO] Task succeeded: Blastn
[2023-06-16 19:12:03,002] [INFO] Selected 23 target genomes.
[2023-06-16 19:12:03,002] [INFO] Target genome list was writen to GCA_009779675.1_ASM977967v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:12:03,044] [INFO] Task started: fastANI
[2023-06-16 19:12:03,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg071cd1af-1f23-444c-9da7-9d0a6438b7b4/GCA_009779675.1_ASM977967v1_genomic.fna.gz --refList GCA_009779675.1_ASM977967v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009779675.1_ASM977967v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:12:15,485] [INFO] Task succeeded: fastANI
[2023-06-16 19:12:15,496] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:12:15,496] [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_009779675.1	s__WRDS01 sp009779675	100.0	574	578	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__PHET01;g__WRDS01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011331305.1	s__DSSC01 sp011331305	77.0557	69	578	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__PHET01;g__DSSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859265.1	s__SKKZ01 sp014859265	76.4346	56	578	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__SLCP01;g__SKKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213085.1	s__JACRBU01 sp016213085	76.3348	60	578	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__JACRBU01;g__JACRBU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347725.1	s__UBA2272 sp002347725	76.1224	52	578	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__UBA2272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015351705.1	s__JADIIM01 sp015351705	76.0096	59	578	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__UBA2279;g__JADIIM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:12:15,499] [INFO] GTDB search result was written to GCA_009779675.1_ASM977967v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:12:15,500] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:12:15,508] [INFO] DFAST_QC result json was written to GCA_009779675.1_ASM977967v1_genomic.fna/dqc_result.json
[2023-06-16 19:12:15,508] [INFO] DFAST_QC completed!
[2023-06-16 19:12:15,508] [INFO] Total running time: 0h1m0s