[2023-06-05 18:42:59,551] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:42:59,553] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:42:59,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgb615edad-2369-4543-8c57-77ddf4f03543/dqc_reference
[2023-06-05 18:43:00,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:43:00,938] [INFO] Task started: Prodigal
[2023-06-05 18:43:00,938] [INFO] Running command: gunzip -c /var/lib/cwl/stga43b6701-93fc-4a09-b3ed-f9bea7c96a3c/GCA_010032425.1_ASM1003242v1_genomic.fna.gz | prodigal -d GCA_010032425.1_ASM1003242v1_genomic.fna/cds.fna -a GCA_010032425.1_ASM1003242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:43:07,253] [INFO] Task succeeded: Prodigal
[2023-06-05 18:43:07,253] [INFO] Task started: HMMsearch
[2023-06-05 18:43:07,253] [INFO] Running command: hmmsearch --tblout GCA_010032425.1_ASM1003242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb615edad-2369-4543-8c57-77ddf4f03543/dqc_reference/reference_markers.hmm GCA_010032425.1_ASM1003242v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:43:07,435] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:43:07,436] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga43b6701-93fc-4a09-b3ed-f9bea7c96a3c/GCA_010032425.1_ASM1003242v1_genomic.fna.gz]
[2023-06-05 18:43:07,460] [INFO] Query marker FASTA was written to GCA_010032425.1_ASM1003242v1_genomic.fna/markers.fasta
[2023-06-05 18:43:07,461] [INFO] Task started: Blastn
[2023-06-05 18:43:07,461] [INFO] Running command: blastn -query GCA_010032425.1_ASM1003242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb615edad-2369-4543-8c57-77ddf4f03543/dqc_reference/reference_markers.fasta -out GCA_010032425.1_ASM1003242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:43:08,051] [INFO] Task succeeded: Blastn
[2023-06-05 18:43:08,055] [INFO] Selected 30 target genomes.
[2023-06-05 18:43:08,055] [INFO] Target genome list was writen to GCA_010032425.1_ASM1003242v1_genomic.fna/target_genomes.txt
[2023-06-05 18:43:08,062] [INFO] Task started: fastANI
[2023-06-05 18:43:08,062] [INFO] Running command: fastANI --query /var/lib/cwl/stga43b6701-93fc-4a09-b3ed-f9bea7c96a3c/GCA_010032425.1_ASM1003242v1_genomic.fna.gz --refList GCA_010032425.1_ASM1003242v1_genomic.fna/target_genomes.txt --output GCA_010032425.1_ASM1003242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:43:25,788] [INFO] Task succeeded: fastANI
[2023-06-05 18:43:25,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb615edad-2369-4543-8c57-77ddf4f03543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:43:25,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb615edad-2369-4543-8c57-77ddf4f03543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:43:25,790] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:43:25,790] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:43:25,790] [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
--------------------------------------------------------------------------------
[2023-06-05 18:43:25,791] [INFO] DFAST Taxonomy check result was written to GCA_010032425.1_ASM1003242v1_genomic.fna/tc_result.tsv
[2023-06-05 18:43:25,792] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:43:25,792] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:43:25,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb615edad-2369-4543-8c57-77ddf4f03543/dqc_reference/checkm_data
[2023-06-05 18:43:25,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:43:25,824] [INFO] Task started: CheckM
[2023-06-05 18:43:25,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010032425.1_ASM1003242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010032425.1_ASM1003242v1_genomic.fna/checkm_input GCA_010032425.1_ASM1003242v1_genomic.fna/checkm_result
[2023-06-05 18:43:49,823] [INFO] Task succeeded: CheckM
[2023-06-05 18:43:49,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:43:49,840] [INFO] ===== Completeness check finished =====
[2023-06-05 18:43:49,841] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:43:49,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010032425.1_ASM1003242v1_genomic.fna/markers.fasta)
[2023-06-05 18:43:49,842] [INFO] Task started: Blastn
[2023-06-05 18:43:49,842] [INFO] Running command: blastn -query GCA_010032425.1_ASM1003242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb615edad-2369-4543-8c57-77ddf4f03543/dqc_reference/reference_markers_gtdb.fasta -out GCA_010032425.1_ASM1003242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:43:51,009] [INFO] Task succeeded: Blastn
[2023-06-05 18:43:51,013] [INFO] Selected 22 target genomes.
[2023-06-05 18:43:51,013] [INFO] Target genome list was writen to GCA_010032425.1_ASM1003242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:43:51,030] [INFO] Task started: fastANI
[2023-06-05 18:43:51,031] [INFO] Running command: fastANI --query /var/lib/cwl/stga43b6701-93fc-4a09-b3ed-f9bea7c96a3c/GCA_010032425.1_ASM1003242v1_genomic.fna.gz --refList GCA_010032425.1_ASM1003242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010032425.1_ASM1003242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:44:07,456] [INFO] Task succeeded: fastANI
[2023-06-05 18:44:07,459] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:44:07,459] [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_001510135.1	s__LFER01 sp001510135	97.6838	375	458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LFER01	95.0	98.63	96.26	0.85	0.78	7	conclusive
--------------------------------------------------------------------------------
[2023-06-05 18:44:07,460] [INFO] GTDB search result was written to GCA_010032425.1_ASM1003242v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:44:07,461] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:44:07,463] [INFO] DFAST_QC result json was written to GCA_010032425.1_ASM1003242v1_genomic.fna/dqc_result.json
[2023-06-05 18:44:07,463] [INFO] DFAST_QC completed!
[2023-06-05 18:44:07,463] [INFO] Total running time: 0h1m8s