[2023-06-18 17:33:59,932] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:33:59,935] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:33:59,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg28418c6a-1017-403b-9273-d9695d5b782d/dqc_reference
[2023-06-18 17:34:01,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:34:01,166] [INFO] Task started: Prodigal
[2023-06-18 17:34:01,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a7703bf-1f39-40d0-b4b6-f54e4240cfa5/GCA_018656725.1_ASM1865672v1_genomic.fna.gz | prodigal -d GCA_018656725.1_ASM1865672v1_genomic.fna/cds.fna -a GCA_018656725.1_ASM1865672v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:34:07,957] [INFO] Task succeeded: Prodigal
[2023-06-18 17:34:07,957] [INFO] Task started: HMMsearch
[2023-06-18 17:34:07,958] [INFO] Running command: hmmsearch --tblout GCA_018656725.1_ASM1865672v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28418c6a-1017-403b-9273-d9695d5b782d/dqc_reference/reference_markers.hmm GCA_018656725.1_ASM1865672v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:34:08,207] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:34:08,210] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1a7703bf-1f39-40d0-b4b6-f54e4240cfa5/GCA_018656725.1_ASM1865672v1_genomic.fna.gz]
[2023-06-18 17:34:08,240] [INFO] Query marker FASTA was written to GCA_018656725.1_ASM1865672v1_genomic.fna/markers.fasta
[2023-06-18 17:34:08,240] [INFO] Task started: Blastn
[2023-06-18 17:34:08,240] [INFO] Running command: blastn -query GCA_018656725.1_ASM1865672v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28418c6a-1017-403b-9273-d9695d5b782d/dqc_reference/reference_markers.fasta -out GCA_018656725.1_ASM1865672v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:34:08,826] [INFO] Task succeeded: Blastn
[2023-06-18 17:34:08,832] [INFO] Selected 12 target genomes.
[2023-06-18 17:34:08,833] [INFO] Target genome list was writen to GCA_018656725.1_ASM1865672v1_genomic.fna/target_genomes.txt
[2023-06-18 17:34:08,836] [INFO] Task started: fastANI
[2023-06-18 17:34:08,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a7703bf-1f39-40d0-b4b6-f54e4240cfa5/GCA_018656725.1_ASM1865672v1_genomic.fna.gz --refList GCA_018656725.1_ASM1865672v1_genomic.fna/target_genomes.txt --output GCA_018656725.1_ASM1865672v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:34:16,426] [INFO] Task succeeded: fastANI
[2023-06-18 17:34:16,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28418c6a-1017-403b-9273-d9695d5b782d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:34:16,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28418c6a-1017-403b-9273-d9695d5b782d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:34:16,428] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:34:16,428] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 17:34:16,428] [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
--------------------------------------------------------------------------------
[2023-06-18 17:34:16,430] [INFO] DFAST Taxonomy check result was written to GCA_018656725.1_ASM1865672v1_genomic.fna/tc_result.tsv
[2023-06-18 17:34:16,431] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:34:16,431] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:34:16,431] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28418c6a-1017-403b-9273-d9695d5b782d/dqc_reference/checkm_data
[2023-06-18 17:34:16,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:34:16,466] [INFO] Task started: CheckM
[2023-06-18 17:34:16,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018656725.1_ASM1865672v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018656725.1_ASM1865672v1_genomic.fna/checkm_input GCA_018656725.1_ASM1865672v1_genomic.fna/checkm_result
[2023-06-18 17:34:44,373] [INFO] Task succeeded: CheckM
[2023-06-18 17:34:44,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:34:44,396] [INFO] ===== Completeness check finished =====
[2023-06-18 17:34:44,396] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:34:44,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018656725.1_ASM1865672v1_genomic.fna/markers.fasta)
[2023-06-18 17:34:44,397] [INFO] Task started: Blastn
[2023-06-18 17:34:44,397] [INFO] Running command: blastn -query GCA_018656725.1_ASM1865672v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28418c6a-1017-403b-9273-d9695d5b782d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018656725.1_ASM1865672v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:34:45,192] [INFO] Task succeeded: Blastn
[2023-06-18 17:34:45,198] [INFO] Selected 17 target genomes.
[2023-06-18 17:34:45,198] [INFO] Target genome list was writen to GCA_018656725.1_ASM1865672v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:34:45,208] [INFO] Task started: fastANI
[2023-06-18 17:34:45,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a7703bf-1f39-40d0-b4b6-f54e4240cfa5/GCA_018656725.1_ASM1865672v1_genomic.fna.gz --refList GCA_018656725.1_ASM1865672v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018656725.1_ASM1865672v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:34:53,133] [INFO] Task succeeded: fastANI
[2023-06-18 17:34:53,142] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:34:53,142] [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_018650185.1	s__GCA-2730555 sp018650185	99.6798	700	752	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.67	99.66	0.92	0.91	4	conclusive
GCA_002730555.1	s__GCA-2730555 sp002730555	78.3865	334	752	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.68	99.68	0.93	0.93	2	-
GCA_014239685.1	s__GCA-2730555 sp014239685	77.6873	193	752	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:34:53,145] [INFO] GTDB search result was written to GCA_018656725.1_ASM1865672v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:34:53,146] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:34:53,153] [INFO] DFAST_QC result json was written to GCA_018656725.1_ASM1865672v1_genomic.fna/dqc_result.json
[2023-06-18 17:34:53,154] [INFO] DFAST_QC completed!
[2023-06-18 17:34:53,154] [INFO] Total running time: 0h0m53s