[2023-06-28 14:06:29,571] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:06:29,573] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:06:29,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc479fc8-db4e-40a3-b357-16b46d231a0c/dqc_reference
[2023-06-28 14:06:30,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:06:30,821] [INFO] Task started: Prodigal
[2023-06-28 14:06:30,821] [INFO] Running command: gunzip -c /var/lib/cwl/stgddfe23e7-5073-44d4-bccc-fc6c96037f7a/GCA_015067145.1_ASM1506714v1_genomic.fna.gz | prodigal -d GCA_015067145.1_ASM1506714v1_genomic.fna/cds.fna -a GCA_015067145.1_ASM1506714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:06:35,311] [INFO] Task succeeded: Prodigal
[2023-06-28 14:06:35,312] [INFO] Task started: HMMsearch
[2023-06-28 14:06:35,312] [INFO] Running command: hmmsearch --tblout GCA_015067145.1_ASM1506714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc479fc8-db4e-40a3-b357-16b46d231a0c/dqc_reference/reference_markers.hmm GCA_015067145.1_ASM1506714v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:06:35,486] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:06:35,487] [INFO] Found 6/6 markers.
[2023-06-28 14:06:35,512] [INFO] Query marker FASTA was written to GCA_015067145.1_ASM1506714v1_genomic.fna/markers.fasta
[2023-06-28 14:06:35,512] [INFO] Task started: Blastn
[2023-06-28 14:06:35,512] [INFO] Running command: blastn -query GCA_015067145.1_ASM1506714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc479fc8-db4e-40a3-b357-16b46d231a0c/dqc_reference/reference_markers.fasta -out GCA_015067145.1_ASM1506714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:06:36,137] [INFO] Task succeeded: Blastn
[2023-06-28 14:06:36,141] [INFO] Selected 22 target genomes.
[2023-06-28 14:06:36,141] [INFO] Target genome list was writen to GCA_015067145.1_ASM1506714v1_genomic.fna/target_genomes.txt
[2023-06-28 14:06:36,142] [INFO] Task started: fastANI
[2023-06-28 14:06:36,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgddfe23e7-5073-44d4-bccc-fc6c96037f7a/GCA_015067145.1_ASM1506714v1_genomic.fna.gz --refList GCA_015067145.1_ASM1506714v1_genomic.fna/target_genomes.txt --output GCA_015067145.1_ASM1506714v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:06:50,077] [INFO] Task succeeded: fastANI
[2023-06-28 14:06:50,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc479fc8-db4e-40a3-b357-16b46d231a0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:06:50,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc479fc8-db4e-40a3-b357-16b46d231a0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:06:50,082] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:06:50,083] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 14:06:50,083] [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 14:06:50,088] [INFO] DFAST Taxonomy check result was written to GCA_015067145.1_ASM1506714v1_genomic.fna/tc_result.tsv
[2023-06-28 14:06:50,088] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:06:50,089] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:06:50,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc479fc8-db4e-40a3-b357-16b46d231a0c/dqc_reference/checkm_data
[2023-06-28 14:06:50,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:06:50,112] [INFO] Task started: CheckM
[2023-06-28 14:06:50,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015067145.1_ASM1506714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015067145.1_ASM1506714v1_genomic.fna/checkm_input GCA_015067145.1_ASM1506714v1_genomic.fna/checkm_result
[2023-06-28 14:07:09,602] [INFO] Task succeeded: CheckM
[2023-06-28 14:07:09,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:07:09,621] [INFO] ===== Completeness check finished =====
[2023-06-28 14:07:09,621] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:07:09,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015067145.1_ASM1506714v1_genomic.fna/markers.fasta)
[2023-06-28 14:07:09,622] [INFO] Task started: Blastn
[2023-06-28 14:07:09,622] [INFO] Running command: blastn -query GCA_015067145.1_ASM1506714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc479fc8-db4e-40a3-b357-16b46d231a0c/dqc_reference/reference_markers_gtdb.fasta -out GCA_015067145.1_ASM1506714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:07:10,623] [INFO] Task succeeded: Blastn
[2023-06-28 14:07:10,628] [INFO] Selected 8 target genomes.
[2023-06-28 14:07:10,628] [INFO] Target genome list was writen to GCA_015067145.1_ASM1506714v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:07:10,629] [INFO] Task started: fastANI
[2023-06-28 14:07:10,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgddfe23e7-5073-44d4-bccc-fc6c96037f7a/GCA_015067145.1_ASM1506714v1_genomic.fna.gz --refList GCA_015067145.1_ASM1506714v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015067145.1_ASM1506714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:07:13,789] [INFO] Task succeeded: fastANI
[2023-06-28 14:07:13,798] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:07:13,798] [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_015067145.1	s__RGIG3102 sp015067145	100.0	585	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017435045.1	s__RGIG3102 sp017435045	85.0874	419	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436765.1	s__RGIG3102 sp017436765	84.8782	401	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017442085.1	s__RGIG3102 sp017442085	83.6793	371	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017505635.1	s__RGIG3102 sp017505635	83.5784	386	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067245.1	s__RGIG3102 sp015067245	83.0899	323	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018109965.1	s__RGIG3102 sp018109965	82.2544	250	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067215.1	s__RGIG3102 sp015067215	81.4382	300	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG3102	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:07:13,800] [INFO] GTDB search result was written to GCA_015067145.1_ASM1506714v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:07:13,800] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:07:13,803] [INFO] DFAST_QC result json was written to GCA_015067145.1_ASM1506714v1_genomic.fna/dqc_result.json
[2023-06-28 14:07:13,803] [INFO] DFAST_QC completed!
[2023-06-28 14:07:13,803] [INFO] Total running time: 0h0m44s