[2023-06-30 15:08:57,007] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:08:57,017] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:08:57,017] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d32d25c-295c-41ed-a40d-e964f222a73a/dqc_reference
[2023-06-30 15:08:58,942] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:08:58,943] [INFO] Task started: Prodigal
[2023-06-30 15:08:58,944] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa890774-5b42-4438-856b-2c41f3bf1f2e/GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna.gz | prodigal -d GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/cds.fna -a GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:09:02,028] [INFO] Task succeeded: Prodigal
[2023-06-30 15:09:02,029] [INFO] Task started: HMMsearch
[2023-06-30 15:09:02,029] [INFO] Running command: hmmsearch --tblout GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d32d25c-295c-41ed-a40d-e964f222a73a/dqc_reference/reference_markers.hmm GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:09:02,207] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:09:02,208] [INFO] Found 6/6 markers.
[2023-06-30 15:09:02,226] [INFO] Query marker FASTA was written to GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/markers.fasta
[2023-06-30 15:09:02,227] [INFO] Task started: Blastn
[2023-06-30 15:09:02,227] [INFO] Running command: blastn -query GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d32d25c-295c-41ed-a40d-e964f222a73a/dqc_reference/reference_markers.fasta -out GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:09:03,125] [INFO] Task succeeded: Blastn
[2023-06-30 15:09:03,129] [INFO] Selected 19 target genomes.
[2023-06-30 15:09:03,129] [INFO] Target genome list was writen to GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/target_genomes.txt
[2023-06-30 15:09:03,135] [INFO] Task started: fastANI
[2023-06-30 15:09:03,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa890774-5b42-4438-856b-2c41f3bf1f2e/GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna.gz --refList GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/target_genomes.txt --output GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:09:16,851] [INFO] Task succeeded: fastANI
[2023-06-30 15:09:16,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d32d25c-295c-41ed-a40d-e964f222a73a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:09:16,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d32d25c-295c-41ed-a40d-e964f222a73a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:09:16,855] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:09:16,855] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 15:09:16,856] [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
--------------------------------------------------------------------------------
[2023-06-30 15:09:16,858] [INFO] DFAST Taxonomy check result was written to GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/tc_result.tsv
[2023-06-30 15:09:16,859] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:09:16,859] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:09:16,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d32d25c-295c-41ed-a40d-e964f222a73a/dqc_reference/checkm_data
[2023-06-30 15:09:16,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:09:16,882] [INFO] Task started: CheckM
[2023-06-30 15:09:16,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/checkm_input GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/checkm_result
[2023-06-30 15:09:33,614] [INFO] Task succeeded: CheckM
[2023-06-30 15:09:33,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.87%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:09:33,639] [INFO] ===== Completeness check finished =====
[2023-06-30 15:09:33,640] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:09:33,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/markers.fasta)
[2023-06-30 15:09:33,641] [INFO] Task started: Blastn
[2023-06-30 15:09:33,641] [INFO] Running command: blastn -query GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d32d25c-295c-41ed-a40d-e964f222a73a/dqc_reference/reference_markers_gtdb.fasta -out GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:09:34,575] [INFO] Task succeeded: Blastn
[2023-06-30 15:09:34,579] [INFO] Selected 23 target genomes.
[2023-06-30 15:09:34,579] [INFO] Target genome list was writen to GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:09:34,592] [INFO] Task started: fastANI
[2023-06-30 15:09:34,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa890774-5b42-4438-856b-2c41f3bf1f2e/GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna.gz --refList GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/target_genomes_gtdb.txt --output GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:09:42,616] [INFO] Task succeeded: fastANI
[2023-06-30 15:09:42,621] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:09:42,621] [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_903871335.1	s__RAAP-2 sp903871335	99.5827	121	124	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.85	98.60	0.98	0.96	25	conclusive
--------------------------------------------------------------------------------
[2023-06-30 15:09:42,624] [INFO] GTDB search result was written to GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/result_gtdb.tsv
[2023-06-30 15:09:42,624] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:09:42,628] [INFO] DFAST_QC result json was written to GCA_903848285.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0709_genomic.fna/dqc_result.json
[2023-06-30 15:09:42,628] [INFO] DFAST_QC completed!
[2023-06-30 15:09:42,628] [INFO] Total running time: 0h0m46s