[2023-06-13 22:53:34,563] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:53:34,565] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:53:34,566] [INFO] DQC Reference Directory: /var/lib/cwl/stgb231fc19-0f52-477b-92be-5bbb96c2c5fa/dqc_reference
[2023-06-13 22:53:36,196] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:53:36,197] [INFO] Task started: Prodigal
[2023-06-13 22:53:36,197] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe91fdea-c1fc-41aa-811c-8aedf61cba1d/GCA_022866485.1_ASM2286648v1_genomic.fna.gz | prodigal -d GCA_022866485.1_ASM2286648v1_genomic.fna/cds.fna -a GCA_022866485.1_ASM2286648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:53:45,113] [INFO] Task succeeded: Prodigal
[2023-06-13 22:53:45,113] [INFO] Task started: HMMsearch
[2023-06-13 22:53:45,114] [INFO] Running command: hmmsearch --tblout GCA_022866485.1_ASM2286648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb231fc19-0f52-477b-92be-5bbb96c2c5fa/dqc_reference/reference_markers.hmm GCA_022866485.1_ASM2286648v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:53:45,392] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:53:45,394] [INFO] Found 6/6 markers.
[2023-06-13 22:53:45,439] [INFO] Query marker FASTA was written to GCA_022866485.1_ASM2286648v1_genomic.fna/markers.fasta
[2023-06-13 22:53:45,439] [INFO] Task started: Blastn
[2023-06-13 22:53:45,439] [INFO] Running command: blastn -query GCA_022866485.1_ASM2286648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb231fc19-0f52-477b-92be-5bbb96c2c5fa/dqc_reference/reference_markers.fasta -out GCA_022866485.1_ASM2286648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:53:46,016] [INFO] Task succeeded: Blastn
[2023-06-13 22:53:46,020] [INFO] Selected 16 target genomes.
[2023-06-13 22:53:46,021] [INFO] Target genome list was writen to GCA_022866485.1_ASM2286648v1_genomic.fna/target_genomes.txt
[2023-06-13 22:53:46,024] [INFO] Task started: fastANI
[2023-06-13 22:53:46,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe91fdea-c1fc-41aa-811c-8aedf61cba1d/GCA_022866485.1_ASM2286648v1_genomic.fna.gz --refList GCA_022866485.1_ASM2286648v1_genomic.fna/target_genomes.txt --output GCA_022866485.1_ASM2286648v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:53:56,877] [INFO] Task succeeded: fastANI
[2023-06-13 22:53:56,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb231fc19-0f52-477b-92be-5bbb96c2c5fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:53:56,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb231fc19-0f52-477b-92be-5bbb96c2c5fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:53:56,880] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:53:56,881] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 22:53:56,881] [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
--------------------------------------------------------------------------------
[2023-06-13 22:53:56,884] [INFO] DFAST Taxonomy check result was written to GCA_022866485.1_ASM2286648v1_genomic.fna/tc_result.tsv
[2023-06-13 22:53:56,884] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:53:56,885] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:53:56,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb231fc19-0f52-477b-92be-5bbb96c2c5fa/dqc_reference/checkm_data
[2023-06-13 22:53:56,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:53:56,941] [INFO] Task started: CheckM
[2023-06-13 22:53:56,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022866485.1_ASM2286648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022866485.1_ASM2286648v1_genomic.fna/checkm_input GCA_022866485.1_ASM2286648v1_genomic.fna/checkm_result
[2023-06-13 22:54:29,670] [INFO] Task succeeded: CheckM
[2023-06-13 22:54:29,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-13 22:54:29,698] [INFO] ===== Completeness check finished =====
[2023-06-13 22:54:29,698] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:54:29,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022866485.1_ASM2286648v1_genomic.fna/markers.fasta)
[2023-06-13 22:54:29,699] [INFO] Task started: Blastn
[2023-06-13 22:54:29,699] [INFO] Running command: blastn -query GCA_022866485.1_ASM2286648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb231fc19-0f52-477b-92be-5bbb96c2c5fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_022866485.1_ASM2286648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:54:30,485] [INFO] Task succeeded: Blastn
[2023-06-13 22:54:30,491] [INFO] Selected 19 target genomes.
[2023-06-13 22:54:30,491] [INFO] Target genome list was writen to GCA_022866485.1_ASM2286648v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:54:30,630] [INFO] Task started: fastANI
[2023-06-13 22:54:30,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe91fdea-c1fc-41aa-811c-8aedf61cba1d/GCA_022866485.1_ASM2286648v1_genomic.fna.gz --refList GCA_022866485.1_ASM2286648v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022866485.1_ASM2286648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:54:40,144] [INFO] Task succeeded: fastANI
[2023-06-13 22:54:40,147] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 22:54:40,147] [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
--------------------------------------------------------------------------------
[2023-06-13 22:54:40,150] [INFO] GTDB search result was written to GCA_022866485.1_ASM2286648v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:54:40,151] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:54:40,154] [INFO] DFAST_QC result json was written to GCA_022866485.1_ASM2286648v1_genomic.fna/dqc_result.json
[2023-06-13 22:54:40,155] [INFO] DFAST_QC completed!
[2023-06-13 22:54:40,155] [INFO] Total running time: 0h1m6s