[2023-06-28 05:38:44,435] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:38:44,438] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:38:44,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg06807aaf-2dd1-483c-8f4b-c3fcb469f860/dqc_reference
[2023-06-28 05:38:46,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:38:46,465] [INFO] Task started: Prodigal
[2023-06-28 05:38:46,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg515a71c0-6af4-4b7f-913f-3d09f0186ef2/GCA_017529085.1_ASM1752908v1_genomic.fna.gz | prodigal -d GCA_017529085.1_ASM1752908v1_genomic.fna/cds.fna -a GCA_017529085.1_ASM1752908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:38:51,822] [INFO] Task succeeded: Prodigal
[2023-06-28 05:38:51,823] [INFO] Task started: HMMsearch
[2023-06-28 05:38:51,823] [INFO] Running command: hmmsearch --tblout GCA_017529085.1_ASM1752908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06807aaf-2dd1-483c-8f4b-c3fcb469f860/dqc_reference/reference_markers.hmm GCA_017529085.1_ASM1752908v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:38:52,060] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:38:52,062] [INFO] Found 6/6 markers.
[2023-06-28 05:38:52,092] [INFO] Query marker FASTA was written to GCA_017529085.1_ASM1752908v1_genomic.fna/markers.fasta
[2023-06-28 05:38:52,092] [INFO] Task started: Blastn
[2023-06-28 05:38:52,092] [INFO] Running command: blastn -query GCA_017529085.1_ASM1752908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06807aaf-2dd1-483c-8f4b-c3fcb469f860/dqc_reference/reference_markers.fasta -out GCA_017529085.1_ASM1752908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:38:52,667] [INFO] Task succeeded: Blastn
[2023-06-28 05:38:52,676] [INFO] Selected 21 target genomes.
[2023-06-28 05:38:52,677] [INFO] Target genome list was writen to GCA_017529085.1_ASM1752908v1_genomic.fna/target_genomes.txt
[2023-06-28 05:38:52,679] [INFO] Task started: fastANI
[2023-06-28 05:38:52,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg515a71c0-6af4-4b7f-913f-3d09f0186ef2/GCA_017529085.1_ASM1752908v1_genomic.fna.gz --refList GCA_017529085.1_ASM1752908v1_genomic.fna/target_genomes.txt --output GCA_017529085.1_ASM1752908v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:39:02,798] [INFO] Task succeeded: fastANI
[2023-06-28 05:39:02,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06807aaf-2dd1-483c-8f4b-c3fcb469f860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:39:02,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06807aaf-2dd1-483c-8f4b-c3fcb469f860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:39:02,801] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:39:02,801] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:39:02,801] [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 05:39:02,804] [INFO] DFAST Taxonomy check result was written to GCA_017529085.1_ASM1752908v1_genomic.fna/tc_result.tsv
[2023-06-28 05:39:02,804] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:39:02,805] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:39:02,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06807aaf-2dd1-483c-8f4b-c3fcb469f860/dqc_reference/checkm_data
[2023-06-28 05:39:02,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:39:02,841] [INFO] Task started: CheckM
[2023-06-28 05:39:02,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017529085.1_ASM1752908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017529085.1_ASM1752908v1_genomic.fna/checkm_input GCA_017529085.1_ASM1752908v1_genomic.fna/checkm_result
[2023-06-28 05:39:25,652] [INFO] Task succeeded: CheckM
[2023-06-28 05:39:25,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 05:39:25,677] [INFO] ===== Completeness check finished =====
[2023-06-28 05:39:25,677] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:39:25,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017529085.1_ASM1752908v1_genomic.fna/markers.fasta)
[2023-06-28 05:39:25,678] [INFO] Task started: Blastn
[2023-06-28 05:39:25,678] [INFO] Running command: blastn -query GCA_017529085.1_ASM1752908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06807aaf-2dd1-483c-8f4b-c3fcb469f860/dqc_reference/reference_markers_gtdb.fasta -out GCA_017529085.1_ASM1752908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:39:26,487] [INFO] Task succeeded: Blastn
[2023-06-28 05:39:26,492] [INFO] Selected 18 target genomes.
[2023-06-28 05:39:26,492] [INFO] Target genome list was writen to GCA_017529085.1_ASM1752908v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:39:26,506] [INFO] Task started: fastANI
[2023-06-28 05:39:26,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg515a71c0-6af4-4b7f-913f-3d09f0186ef2/GCA_017529085.1_ASM1752908v1_genomic.fna.gz --refList GCA_017529085.1_ASM1752908v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017529085.1_ASM1752908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:39:34,405] [INFO] Task succeeded: fastANI
[2023-06-28 05:39:34,411] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:39:34,412] [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_017529085.1	s__RGIG9201 sp017529085	100.0	554	562	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RGIG9201	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017634675.1	s__RGIG9201 sp017634675	86.5158	341	562	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RGIG9201	95.0	96.58	96.58	0.73	0.73	2	-
GCA_017635875.1	s__RGIG9201 sp017635875	78.5856	128	562	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RGIG9201	95.0	98.62	98.62	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-28 05:39:34,414] [INFO] GTDB search result was written to GCA_017529085.1_ASM1752908v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:39:34,414] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:39:34,417] [INFO] DFAST_QC result json was written to GCA_017529085.1_ASM1752908v1_genomic.fna/dqc_result.json
[2023-06-28 05:39:34,417] [INFO] DFAST_QC completed!
[2023-06-28 05:39:34,417] [INFO] Total running time: 0h0m50s