[2023-06-28 20:26:36,272] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:26:36,274] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:26:36,274] [INFO] DQC Reference Directory: /var/lib/cwl/stg62b2a657-8b89-4825-b280-be9348dda401/dqc_reference
[2023-06-28 20:26:38,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:26:38,900] [INFO] Task started: Prodigal
[2023-06-28 20:26:38,901] [INFO] Running command: gunzip -c /var/lib/cwl/stg03aada4f-1497-4694-ad13-8deea77b5a74/GCA_017396845.1_ASM1739684v1_genomic.fna.gz | prodigal -d GCA_017396845.1_ASM1739684v1_genomic.fna/cds.fna -a GCA_017396845.1_ASM1739684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:26:45,748] [INFO] Task succeeded: Prodigal
[2023-06-28 20:26:45,748] [INFO] Task started: HMMsearch
[2023-06-28 20:26:45,749] [INFO] Running command: hmmsearch --tblout GCA_017396845.1_ASM1739684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62b2a657-8b89-4825-b280-be9348dda401/dqc_reference/reference_markers.hmm GCA_017396845.1_ASM1739684v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:26:45,975] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:26:45,977] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg03aada4f-1497-4694-ad13-8deea77b5a74/GCA_017396845.1_ASM1739684v1_genomic.fna.gz]
[2023-06-28 20:26:46,006] [INFO] Query marker FASTA was written to GCA_017396845.1_ASM1739684v1_genomic.fna/markers.fasta
[2023-06-28 20:26:46,007] [INFO] Task started: Blastn
[2023-06-28 20:26:46,007] [INFO] Running command: blastn -query GCA_017396845.1_ASM1739684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62b2a657-8b89-4825-b280-be9348dda401/dqc_reference/reference_markers.fasta -out GCA_017396845.1_ASM1739684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:26:46,567] [INFO] Task succeeded: Blastn
[2023-06-28 20:26:46,573] [INFO] Selected 18 target genomes.
[2023-06-28 20:26:46,573] [INFO] Target genome list was writen to GCA_017396845.1_ASM1739684v1_genomic.fna/target_genomes.txt
[2023-06-28 20:26:46,577] [INFO] Task started: fastANI
[2023-06-28 20:26:46,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg03aada4f-1497-4694-ad13-8deea77b5a74/GCA_017396845.1_ASM1739684v1_genomic.fna.gz --refList GCA_017396845.1_ASM1739684v1_genomic.fna/target_genomes.txt --output GCA_017396845.1_ASM1739684v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:26:56,850] [INFO] Task succeeded: fastANI
[2023-06-28 20:26:56,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62b2a657-8b89-4825-b280-be9348dda401/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:26:56,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62b2a657-8b89-4825-b280-be9348dda401/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:26:56,854] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:26:56,854] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 20:26:56,854] [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 20:26:56,856] [INFO] DFAST Taxonomy check result was written to GCA_017396845.1_ASM1739684v1_genomic.fna/tc_result.tsv
[2023-06-28 20:26:56,857] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:26:56,857] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:26:56,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62b2a657-8b89-4825-b280-be9348dda401/dqc_reference/checkm_data
[2023-06-28 20:26:56,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:26:56,896] [INFO] Task started: CheckM
[2023-06-28 20:26:56,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017396845.1_ASM1739684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017396845.1_ASM1739684v1_genomic.fna/checkm_input GCA_017396845.1_ASM1739684v1_genomic.fna/checkm_result
[2023-06-28 20:27:23,121] [INFO] Task succeeded: CheckM
[2023-06-28 20:27:23,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.87%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:27:23,153] [INFO] ===== Completeness check finished =====
[2023-06-28 20:27:23,153] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:27:23,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017396845.1_ASM1739684v1_genomic.fna/markers.fasta)
[2023-06-28 20:27:23,154] [INFO] Task started: Blastn
[2023-06-28 20:27:23,154] [INFO] Running command: blastn -query GCA_017396845.1_ASM1739684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62b2a657-8b89-4825-b280-be9348dda401/dqc_reference/reference_markers_gtdb.fasta -out GCA_017396845.1_ASM1739684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:27:23,968] [INFO] Task succeeded: Blastn
[2023-06-28 20:27:23,973] [INFO] Selected 13 target genomes.
[2023-06-28 20:27:23,973] [INFO] Target genome list was writen to GCA_017396845.1_ASM1739684v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:27:23,981] [INFO] Task started: fastANI
[2023-06-28 20:27:23,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg03aada4f-1497-4694-ad13-8deea77b5a74/GCA_017396845.1_ASM1739684v1_genomic.fna.gz --refList GCA_017396845.1_ASM1739684v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017396845.1_ASM1739684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:27:30,475] [INFO] Task succeeded: fastANI
[2023-06-28 20:27:30,483] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:27:30,483] [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_017396845.1	s__SFHK01 sp017396845	100.0	855	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017522345.1	s__SFHK01 sp017522345	79.0727	273	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056255.1	s__SFHK01 sp015056255	78.9005	273	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296675.1	s__SFHK01 sp016296675	78.543	250	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	96.60	96.60	0.77	0.77	2	-
GCA_004556395.1	s__SFHK01 sp004556395	77.3991	220	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFHK01	95.0	99.09	98.81	0.92	0.90	3	-
GCA_902796025.1	s__RUG14130 sp902796025	77.2342	87	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG14130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793325.1	s__UBA2862 sp902793325	76.4389	54	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412445.1	s__RUG14130 sp017412445	76.2836	51	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG14130	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:27:30,487] [INFO] GTDB search result was written to GCA_017396845.1_ASM1739684v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:27:30,487] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:27:30,491] [INFO] DFAST_QC result json was written to GCA_017396845.1_ASM1739684v1_genomic.fna/dqc_result.json
[2023-06-28 20:27:30,492] [INFO] DFAST_QC completed!
[2023-06-28 20:27:30,492] [INFO] Total running time: 0h0m54s