[2023-06-28 08:10:59,366] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:10:59,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:10:59,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f59b240-edda-4c31-99b1-2442a5b04ff1/dqc_reference
[2023-06-28 08:11:00,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:11:00,638] [INFO] Task started: Prodigal
[2023-06-28 08:11:00,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg1456a794-d37b-48d5-adeb-1d834e9b98b5/GCA_944383975.1_E21_bin145_genomic.fna.gz | prodigal -d GCA_944383975.1_E21_bin145_genomic.fna/cds.fna -a GCA_944383975.1_E21_bin145_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:11:02,558] [INFO] Task succeeded: Prodigal
[2023-06-28 08:11:02,559] [INFO] Task started: HMMsearch
[2023-06-28 08:11:02,559] [INFO] Running command: hmmsearch --tblout GCA_944383975.1_E21_bin145_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f59b240-edda-4c31-99b1-2442a5b04ff1/dqc_reference/reference_markers.hmm GCA_944383975.1_E21_bin145_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:11:02,764] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:11:02,765] [INFO] Found 6/6 markers.
[2023-06-28 08:11:02,781] [INFO] Query marker FASTA was written to GCA_944383975.1_E21_bin145_genomic.fna/markers.fasta
[2023-06-28 08:11:02,781] [INFO] Task started: Blastn
[2023-06-28 08:11:02,781] [INFO] Running command: blastn -query GCA_944383975.1_E21_bin145_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f59b240-edda-4c31-99b1-2442a5b04ff1/dqc_reference/reference_markers.fasta -out GCA_944383975.1_E21_bin145_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:11:03,556] [INFO] Task succeeded: Blastn
[2023-06-28 08:11:03,561] [INFO] Selected 22 target genomes.
[2023-06-28 08:11:03,561] [INFO] Target genome list was writen to GCA_944383975.1_E21_bin145_genomic.fna/target_genomes.txt
[2023-06-28 08:11:03,563] [INFO] Task started: fastANI
[2023-06-28 08:11:03,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg1456a794-d37b-48d5-adeb-1d834e9b98b5/GCA_944383975.1_E21_bin145_genomic.fna.gz --refList GCA_944383975.1_E21_bin145_genomic.fna/target_genomes.txt --output GCA_944383975.1_E21_bin145_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:11:11,712] [INFO] Task succeeded: fastANI
[2023-06-28 08:11:11,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f59b240-edda-4c31-99b1-2442a5b04ff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:11:11,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f59b240-edda-4c31-99b1-2442a5b04ff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:11:11,719] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:11:11,719] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:11:11,720] [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 08:11:11,731] [INFO] DFAST Taxonomy check result was written to GCA_944383975.1_E21_bin145_genomic.fna/tc_result.tsv
[2023-06-28 08:11:11,733] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:11:11,733] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:11:11,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f59b240-edda-4c31-99b1-2442a5b04ff1/dqc_reference/checkm_data
[2023-06-28 08:11:11,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:11:11,759] [INFO] Task started: CheckM
[2023-06-28 08:11:11,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944383975.1_E21_bin145_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944383975.1_E21_bin145_genomic.fna/checkm_input GCA_944383975.1_E21_bin145_genomic.fna/checkm_result
[2023-06-28 08:11:27,351] [INFO] Task succeeded: CheckM
[2023-06-28 08:11:27,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:11:27,374] [INFO] ===== Completeness check finished =====
[2023-06-28 08:11:27,375] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:11:27,375] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944383975.1_E21_bin145_genomic.fna/markers.fasta)
[2023-06-28 08:11:27,375] [INFO] Task started: Blastn
[2023-06-28 08:11:27,375] [INFO] Running command: blastn -query GCA_944383975.1_E21_bin145_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f59b240-edda-4c31-99b1-2442a5b04ff1/dqc_reference/reference_markers_gtdb.fasta -out GCA_944383975.1_E21_bin145_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:11:28,409] [INFO] Task succeeded: Blastn
[2023-06-28 08:11:28,413] [INFO] Selected 18 target genomes.
[2023-06-28 08:11:28,413] [INFO] Target genome list was writen to GCA_944383975.1_E21_bin145_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:11:28,420] [INFO] Task started: fastANI
[2023-06-28 08:11:28,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg1456a794-d37b-48d5-adeb-1d834e9b98b5/GCA_944383975.1_E21_bin145_genomic.fna.gz --refList GCA_944383975.1_E21_bin145_genomic.fna/target_genomes_gtdb.txt --output GCA_944383975.1_E21_bin145_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:11:34,148] [INFO] Task succeeded: fastANI
[2023-06-28 08:11:34,160] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 08:11:34,160] [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_900557645.1	s__Caccovivens sp900557645	82.6307	193	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Caccovivens	95.0	99.83	99.83	0.95	0.95	2	-
GCA_017466725.1	s__Caccovivens sp017466725	77.8917	51	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Caccovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796285.1	s__Caccovivens sp902796285	77.7238	67	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Caccovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621525.1	s__Caccovivens sp017621525	77.3251	59	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Caccovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015069325.1	s__Caccovivens sp015069325	77.2196	72	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Caccovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017464845.1	s__Caccovivens sp017464845	75.9665	50	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Caccovivens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:11:34,162] [INFO] GTDB search result was written to GCA_944383975.1_E21_bin145_genomic.fna/result_gtdb.tsv
[2023-06-28 08:11:34,162] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:11:34,164] [INFO] DFAST_QC result json was written to GCA_944383975.1_E21_bin145_genomic.fna/dqc_result.json
[2023-06-28 08:11:34,164] [INFO] DFAST_QC completed!
[2023-06-28 08:11:34,164] [INFO] Total running time: 0h0m35s