[2023-06-28 10:16:16,755] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:16:16,759] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:16:16,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cc9916c-2324-457f-9bff-605721670fff/dqc_reference
[2023-06-28 10:16:18,080] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:16:18,081] [INFO] Task started: Prodigal
[2023-06-28 10:16:18,081] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e008a43-f490-47d2-a0fc-3513fa7b2c6d/GCA_019310885.1_ASM1931088v1_genomic.fna.gz | prodigal -d GCA_019310885.1_ASM1931088v1_genomic.fna/cds.fna -a GCA_019310885.1_ASM1931088v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:16:23,366] [INFO] Task succeeded: Prodigal
[2023-06-28 10:16:23,366] [INFO] Task started: HMMsearch
[2023-06-28 10:16:23,367] [INFO] Running command: hmmsearch --tblout GCA_019310885.1_ASM1931088v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cc9916c-2324-457f-9bff-605721670fff/dqc_reference/reference_markers.hmm GCA_019310885.1_ASM1931088v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:16:23,604] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:16:23,605] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3e008a43-f490-47d2-a0fc-3513fa7b2c6d/GCA_019310885.1_ASM1931088v1_genomic.fna.gz]
[2023-06-28 10:16:23,637] [INFO] Query marker FASTA was written to GCA_019310885.1_ASM1931088v1_genomic.fna/markers.fasta
[2023-06-28 10:16:23,637] [INFO] Task started: Blastn
[2023-06-28 10:16:23,637] [INFO] Running command: blastn -query GCA_019310885.1_ASM1931088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc9916c-2324-457f-9bff-605721670fff/dqc_reference/reference_markers.fasta -out GCA_019310885.1_ASM1931088v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:24,145] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:24,151] [INFO] Selected 13 target genomes.
[2023-06-28 10:16:24,151] [INFO] Target genome list was writen to GCA_019310885.1_ASM1931088v1_genomic.fna/target_genomes.txt
[2023-06-28 10:16:24,152] [INFO] Task started: fastANI
[2023-06-28 10:16:24,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e008a43-f490-47d2-a0fc-3513fa7b2c6d/GCA_019310885.1_ASM1931088v1_genomic.fna.gz --refList GCA_019310885.1_ASM1931088v1_genomic.fna/target_genomes.txt --output GCA_019310885.1_ASM1931088v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:16:30,153] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:30,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cc9916c-2324-457f-9bff-605721670fff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:16:30,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cc9916c-2324-457f-9bff-605721670fff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:16:30,159] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:16:30,159] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:16:30,160] [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
--------------------------------------------------------------------------------
[2023-06-28 10:16:30,162] [INFO] DFAST Taxonomy check result was written to GCA_019310885.1_ASM1931088v1_genomic.fna/tc_result.tsv
[2023-06-28 10:16:30,163] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:16:30,163] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:16:30,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cc9916c-2324-457f-9bff-605721670fff/dqc_reference/checkm_data
[2023-06-28 10:16:30,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:16:30,204] [INFO] Task started: CheckM
[2023-06-28 10:16:30,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310885.1_ASM1931088v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310885.1_ASM1931088v1_genomic.fna/checkm_input GCA_019310885.1_ASM1931088v1_genomic.fna/checkm_result
[2023-06-28 10:16:52,838] [INFO] Task succeeded: CheckM
[2023-06-28 10:16:52,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:16:52,862] [INFO] ===== Completeness check finished =====
[2023-06-28 10:16:52,863] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:16:52,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310885.1_ASM1931088v1_genomic.fna/markers.fasta)
[2023-06-28 10:16:52,863] [INFO] Task started: Blastn
[2023-06-28 10:16:52,864] [INFO] Running command: blastn -query GCA_019310885.1_ASM1931088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc9916c-2324-457f-9bff-605721670fff/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310885.1_ASM1931088v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:53,347] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:53,353] [INFO] Selected 18 target genomes.
[2023-06-28 10:16:53,353] [INFO] Target genome list was writen to GCA_019310885.1_ASM1931088v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:16:53,360] [INFO] Task started: fastANI
[2023-06-28 10:16:53,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e008a43-f490-47d2-a0fc-3513fa7b2c6d/GCA_019310885.1_ASM1931088v1_genomic.fna.gz --refList GCA_019310885.1_ASM1931088v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310885.1_ASM1931088v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:17:02,422] [INFO] Task succeeded: fastANI
[2023-06-28 10:17:02,427] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:17:02,428] [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_011391835.1	s__JAABPS01 sp011391835	78.3263	131	628	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAABPS01;g__JAABPS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:17:02,430] [INFO] GTDB search result was written to GCA_019310885.1_ASM1931088v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:17:02,431] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:17:02,433] [INFO] DFAST_QC result json was written to GCA_019310885.1_ASM1931088v1_genomic.fna/dqc_result.json
[2023-06-28 10:17:02,434] [INFO] DFAST_QC completed!
[2023-06-28 10:17:02,434] [INFO] Total running time: 0h0m46s