[2023-07-01 05:28:33,996] [INFO] DFAST_QC pipeline started.
[2023-07-01 05:28:34,000] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 05:28:34,000] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e9855a8-c45e-4997-b66b-5377b17548ba/dqc_reference
[2023-07-01 05:28:36,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 05:28:36,270] [INFO] Task started: Prodigal
[2023-07-01 05:28:36,270] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe41b919-d481-4557-af51-ca0b4b44bda6/GCA_019113865.1_ASM1911386v1_genomic.fna.gz | prodigal -d GCA_019113865.1_ASM1911386v1_genomic.fna/cds.fna -a GCA_019113865.1_ASM1911386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 05:28:40,547] [INFO] Task succeeded: Prodigal
[2023-07-01 05:28:40,548] [INFO] Task started: HMMsearch
[2023-07-01 05:28:40,548] [INFO] Running command: hmmsearch --tblout GCA_019113865.1_ASM1911386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e9855a8-c45e-4997-b66b-5377b17548ba/dqc_reference/reference_markers.hmm GCA_019113865.1_ASM1911386v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 05:28:40,775] [INFO] Task succeeded: HMMsearch
[2023-07-01 05:28:40,777] [INFO] Found 6/6 markers.
[2023-07-01 05:28:40,820] [INFO] Query marker FASTA was written to GCA_019113865.1_ASM1911386v1_genomic.fna/markers.fasta
[2023-07-01 05:28:40,821] [INFO] Task started: Blastn
[2023-07-01 05:28:40,821] [INFO] Running command: blastn -query GCA_019113865.1_ASM1911386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e9855a8-c45e-4997-b66b-5377b17548ba/dqc_reference/reference_markers.fasta -out GCA_019113865.1_ASM1911386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:28:41,407] [INFO] Task succeeded: Blastn
[2023-07-01 05:28:41,412] [INFO] Selected 21 target genomes.
[2023-07-01 05:28:41,413] [INFO] Target genome list was writen to GCA_019113865.1_ASM1911386v1_genomic.fna/target_genomes.txt
[2023-07-01 05:28:41,419] [INFO] Task started: fastANI
[2023-07-01 05:28:41,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe41b919-d481-4557-af51-ca0b4b44bda6/GCA_019113865.1_ASM1911386v1_genomic.fna.gz --refList GCA_019113865.1_ASM1911386v1_genomic.fna/target_genomes.txt --output GCA_019113865.1_ASM1911386v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 05:28:57,513] [INFO] Task succeeded: fastANI
[2023-07-01 05:28:57,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e9855a8-c45e-4997-b66b-5377b17548ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 05:28:57,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e9855a8-c45e-4997-b66b-5377b17548ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 05:28:57,541] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 05:28:57,542] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 05:28:57,542] [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
--------------------------------------------------------------------------------
[2023-07-01 05:28:57,544] [INFO] DFAST Taxonomy check result was written to GCA_019113865.1_ASM1911386v1_genomic.fna/tc_result.tsv
[2023-07-01 05:28:57,545] [INFO] ===== Taxonomy check completed =====
[2023-07-01 05:28:57,545] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 05:28:57,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e9855a8-c45e-4997-b66b-5377b17548ba/dqc_reference/checkm_data
[2023-07-01 05:28:57,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 05:28:57,576] [INFO] Task started: CheckM
[2023-07-01 05:28:57,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019113865.1_ASM1911386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019113865.1_ASM1911386v1_genomic.fna/checkm_input GCA_019113865.1_ASM1911386v1_genomic.fna/checkm_result
[2023-07-01 05:29:17,135] [INFO] Task succeeded: CheckM
[2023-07-01 05:29:17,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 05:29:17,157] [INFO] ===== Completeness check finished =====
[2023-07-01 05:29:17,158] [INFO] ===== Start GTDB Search =====
[2023-07-01 05:29:17,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019113865.1_ASM1911386v1_genomic.fna/markers.fasta)
[2023-07-01 05:29:17,159] [INFO] Task started: Blastn
[2023-07-01 05:29:17,159] [INFO] Running command: blastn -query GCA_019113865.1_ASM1911386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e9855a8-c45e-4997-b66b-5377b17548ba/dqc_reference/reference_markers_gtdb.fasta -out GCA_019113865.1_ASM1911386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:29:18,032] [INFO] Task succeeded: Blastn
[2023-07-01 05:29:18,037] [INFO] Selected 22 target genomes.
[2023-07-01 05:29:18,037] [INFO] Target genome list was writen to GCA_019113865.1_ASM1911386v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 05:29:18,051] [INFO] Task started: fastANI
[2023-07-01 05:29:18,051] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe41b919-d481-4557-af51-ca0b4b44bda6/GCA_019113865.1_ASM1911386v1_genomic.fna.gz --refList GCA_019113865.1_ASM1911386v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019113865.1_ASM1911386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 05:29:26,585] [INFO] Task succeeded: fastANI
[2023-07-01 05:29:26,592] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 05:29:26,592] [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
GCF_904419955.1	s__Roslinia caecavium	99.9129	700	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__Roslinia	95.0	99.91	99.91	0.97	0.97	2	conclusive
GCA_019112945.1	s__Monoglobus merdigallinarum	77.3689	58	722	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__Monoglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 05:29:26,638] [INFO] GTDB search result was written to GCA_019113865.1_ASM1911386v1_genomic.fna/result_gtdb.tsv
[2023-07-01 05:29:26,639] [INFO] ===== GTDB Search completed =====
[2023-07-01 05:29:26,642] [INFO] DFAST_QC result json was written to GCA_019113865.1_ASM1911386v1_genomic.fna/dqc_result.json
[2023-07-01 05:29:26,642] [INFO] DFAST_QC completed!
[2023-07-01 05:29:26,642] [INFO] Total running time: 0h0m53s