[2023-06-28 19:49:37,357] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:49:37,360] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:49:37,360] [INFO] DQC Reference Directory: /var/lib/cwl/stge86a6ef6-9ab0-4b1f-b3ab-3a9f65f80af4/dqc_reference
[2023-06-28 19:49:38,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:49:38,755] [INFO] Task started: Prodigal
[2023-06-28 19:49:38,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg78acfb37-7b8b-4bf7-a728-df5480dac2c4/GCA_017539025.1_ASM1753902v1_genomic.fna.gz | prodigal -d GCA_017539025.1_ASM1753902v1_genomic.fna/cds.fna -a GCA_017539025.1_ASM1753902v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:49:44,248] [INFO] Task succeeded: Prodigal
[2023-06-28 19:49:44,249] [INFO] Task started: HMMsearch
[2023-06-28 19:49:44,249] [INFO] Running command: hmmsearch --tblout GCA_017539025.1_ASM1753902v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge86a6ef6-9ab0-4b1f-b3ab-3a9f65f80af4/dqc_reference/reference_markers.hmm GCA_017539025.1_ASM1753902v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:49:44,492] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:49:44,493] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg78acfb37-7b8b-4bf7-a728-df5480dac2c4/GCA_017539025.1_ASM1753902v1_genomic.fna.gz]
[2023-06-28 19:49:44,517] [INFO] Query marker FASTA was written to GCA_017539025.1_ASM1753902v1_genomic.fna/markers.fasta
[2023-06-28 19:49:44,517] [INFO] Task started: Blastn
[2023-06-28 19:49:44,517] [INFO] Running command: blastn -query GCA_017539025.1_ASM1753902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge86a6ef6-9ab0-4b1f-b3ab-3a9f65f80af4/dqc_reference/reference_markers.fasta -out GCA_017539025.1_ASM1753902v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:45,145] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:45,149] [INFO] Selected 23 target genomes.
[2023-06-28 19:49:45,149] [INFO] Target genome list was writen to GCA_017539025.1_ASM1753902v1_genomic.fna/target_genomes.txt
[2023-06-28 19:49:45,158] [INFO] Task started: fastANI
[2023-06-28 19:49:45,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg78acfb37-7b8b-4bf7-a728-df5480dac2c4/GCA_017539025.1_ASM1753902v1_genomic.fna.gz --refList GCA_017539025.1_ASM1753902v1_genomic.fna/target_genomes.txt --output GCA_017539025.1_ASM1753902v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:49:59,861] [INFO] Task succeeded: fastANI
[2023-06-28 19:49:59,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge86a6ef6-9ab0-4b1f-b3ab-3a9f65f80af4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:49:59,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge86a6ef6-9ab0-4b1f-b3ab-3a9f65f80af4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:49:59,864] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:49:59,864] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:49:59,865] [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 19:49:59,866] [INFO] DFAST Taxonomy check result was written to GCA_017539025.1_ASM1753902v1_genomic.fna/tc_result.tsv
[2023-06-28 19:49:59,867] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:49:59,867] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:49:59,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge86a6ef6-9ab0-4b1f-b3ab-3a9f65f80af4/dqc_reference/checkm_data
[2023-06-28 19:49:59,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:49:59,918] [INFO] Task started: CheckM
[2023-06-28 19:49:59,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017539025.1_ASM1753902v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017539025.1_ASM1753902v1_genomic.fna/checkm_input GCA_017539025.1_ASM1753902v1_genomic.fna/checkm_result
[2023-06-28 19:50:24,787] [INFO] Task succeeded: CheckM
[2023-06-28 19:50:24,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:50:24,811] [INFO] ===== Completeness check finished =====
[2023-06-28 19:50:24,812] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:50:24,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017539025.1_ASM1753902v1_genomic.fna/markers.fasta)
[2023-06-28 19:50:24,812] [INFO] Task started: Blastn
[2023-06-28 19:50:24,813] [INFO] Running command: blastn -query GCA_017539025.1_ASM1753902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge86a6ef6-9ab0-4b1f-b3ab-3a9f65f80af4/dqc_reference/reference_markers_gtdb.fasta -out GCA_017539025.1_ASM1753902v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:50:25,621] [INFO] Task succeeded: Blastn
[2023-06-28 19:50:25,626] [INFO] Selected 12 target genomes.
[2023-06-28 19:50:25,627] [INFO] Target genome list was writen to GCA_017539025.1_ASM1753902v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:50:25,629] [INFO] Task started: fastANI
[2023-06-28 19:50:25,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg78acfb37-7b8b-4bf7-a728-df5480dac2c4/GCA_017539025.1_ASM1753902v1_genomic.fna.gz --refList GCA_017539025.1_ASM1753902v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017539025.1_ASM1753902v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:50:30,344] [INFO] Task succeeded: fastANI
[2023-06-28 19:50:30,356] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:50:30,357] [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_017539025.1	s__UBA636 sp017539025	100.0	744	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017454765.1	s__UBA636 sp017454765	81.2426	359	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428765.1	s__UBA636 sp017428765	79.7168	322	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	97.78	97.78	0.93	0.93	2	-
GCA_002362065.1	s__UBA636 sp002362065	79.4439	267	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321955.1	s__UBA636 sp900321955	79.4189	212	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	97.85	96.88	0.77	0.69	28	-
GCA_017432005.1	s__UBA636 sp017432005	79.3984	260	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432895.1	s__UBA636 sp017432895	79.3132	314	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550145.1	s__UBA636 sp017550145	79.2421	285	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017419165.1	s__UBA636 sp017419165	78.9892	241	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017404785.1	s__UBA636 sp017404785	78.6026	148	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803785.1	s__UBA636 sp902803785	78.468	156	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418585.1	s__UBA636 sp017418585	78.1911	144	747	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:50:30,358] [INFO] GTDB search result was written to GCA_017539025.1_ASM1753902v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:50:30,359] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:50:30,362] [INFO] DFAST_QC result json was written to GCA_017539025.1_ASM1753902v1_genomic.fna/dqc_result.json
[2023-06-28 19:50:30,362] [INFO] DFAST_QC completed!
[2023-06-28 19:50:30,362] [INFO] Total running time: 0h0m53s