[2023-06-29 00:04:01,494] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:04:01,497] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:04:01,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fa2f0d1-47a6-42f3-b10e-c75b6f703385/dqc_reference
[2023-06-29 00:04:02,792] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:04:02,793] [INFO] Task started: Prodigal
[2023-06-29 00:04:02,794] [INFO] Running command: gunzip -c /var/lib/cwl/stgc75d1387-c8e9-462e-b442-3161cb353c02/GCA_020060425.1_ASM2006042v1_genomic.fna.gz | prodigal -d GCA_020060425.1_ASM2006042v1_genomic.fna/cds.fna -a GCA_020060425.1_ASM2006042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:04:06,956] [INFO] Task succeeded: Prodigal
[2023-06-29 00:04:06,956] [INFO] Task started: HMMsearch
[2023-06-29 00:04:06,956] [INFO] Running command: hmmsearch --tblout GCA_020060425.1_ASM2006042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fa2f0d1-47a6-42f3-b10e-c75b6f703385/dqc_reference/reference_markers.hmm GCA_020060425.1_ASM2006042v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:04:07,197] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:04:07,198] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc75d1387-c8e9-462e-b442-3161cb353c02/GCA_020060425.1_ASM2006042v1_genomic.fna.gz]
[2023-06-29 00:04:07,229] [INFO] Query marker FASTA was written to GCA_020060425.1_ASM2006042v1_genomic.fna/markers.fasta
[2023-06-29 00:04:07,229] [INFO] Task started: Blastn
[2023-06-29 00:04:07,230] [INFO] Running command: blastn -query GCA_020060425.1_ASM2006042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fa2f0d1-47a6-42f3-b10e-c75b6f703385/dqc_reference/reference_markers.fasta -out GCA_020060425.1_ASM2006042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:04:07,724] [INFO] Task succeeded: Blastn
[2023-06-29 00:04:07,732] [INFO] Selected 11 target genomes.
[2023-06-29 00:04:07,733] [INFO] Target genome list was writen to GCA_020060425.1_ASM2006042v1_genomic.fna/target_genomes.txt
[2023-06-29 00:04:07,737] [INFO] Task started: fastANI
[2023-06-29 00:04:07,737] [INFO] Running command: fastANI --query /var/lib/cwl/stgc75d1387-c8e9-462e-b442-3161cb353c02/GCA_020060425.1_ASM2006042v1_genomic.fna.gz --refList GCA_020060425.1_ASM2006042v1_genomic.fna/target_genomes.txt --output GCA_020060425.1_ASM2006042v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:04:18,834] [INFO] Task succeeded: fastANI
[2023-06-29 00:04:18,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fa2f0d1-47a6-42f3-b10e-c75b6f703385/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:04:18,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fa2f0d1-47a6-42f3-b10e-c75b6f703385/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:04:18,838] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:04:18,838] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:04:18,838] [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
--------------------------------------------------------------------------------
[2023-06-29 00:04:18,844] [INFO] DFAST Taxonomy check result was written to GCA_020060425.1_ASM2006042v1_genomic.fna/tc_result.tsv
[2023-06-29 00:04:18,848] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:04:18,848] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:04:18,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fa2f0d1-47a6-42f3-b10e-c75b6f703385/dqc_reference/checkm_data
[2023-06-29 00:04:18,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:04:18,885] [INFO] Task started: CheckM
[2023-06-29 00:04:18,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020060425.1_ASM2006042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020060425.1_ASM2006042v1_genomic.fna/checkm_input GCA_020060425.1_ASM2006042v1_genomic.fna/checkm_result
[2023-06-29 00:04:38,574] [INFO] Task succeeded: CheckM
[2023-06-29 00:04:38,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:04:38,603] [INFO] ===== Completeness check finished =====
[2023-06-29 00:04:38,603] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:04:38,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020060425.1_ASM2006042v1_genomic.fna/markers.fasta)
[2023-06-29 00:04:38,604] [INFO] Task started: Blastn
[2023-06-29 00:04:38,604] [INFO] Running command: blastn -query GCA_020060425.1_ASM2006042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fa2f0d1-47a6-42f3-b10e-c75b6f703385/dqc_reference/reference_markers_gtdb.fasta -out GCA_020060425.1_ASM2006042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:04:39,068] [INFO] Task succeeded: Blastn
[2023-06-29 00:04:39,076] [INFO] Selected 16 target genomes.
[2023-06-29 00:04:39,076] [INFO] Target genome list was writen to GCA_020060425.1_ASM2006042v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:04:39,088] [INFO] Task started: fastANI
[2023-06-29 00:04:39,088] [INFO] Running command: fastANI --query /var/lib/cwl/stgc75d1387-c8e9-462e-b442-3161cb353c02/GCA_020060425.1_ASM2006042v1_genomic.fna.gz --refList GCA_020060425.1_ASM2006042v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020060425.1_ASM2006042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:04:47,460] [INFO] Task succeeded: fastANI
[2023-06-29 00:04:47,463] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:04:47,463] [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_003604985.1	s__SURF-55 sp003604985	99.7254	409	523	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Ammonifexales;f__Ammonificaceae;g__SURF-55	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-29 00:04:47,468] [INFO] GTDB search result was written to GCA_020060425.1_ASM2006042v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:04:47,469] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:04:47,473] [INFO] DFAST_QC result json was written to GCA_020060425.1_ASM2006042v1_genomic.fna/dqc_result.json
[2023-06-29 00:04:47,473] [INFO] DFAST_QC completed!
[2023-06-29 00:04:47,473] [INFO] Total running time: 0h0m46s