[2023-06-19 11:23:06,792] [INFO] DFAST_QC pipeline started.
[2023-06-19 11:23:06,803] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 11:23:06,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg594601f0-af39-442c-895e-c6651bb078c4/dqc_reference
[2023-06-19 11:23:08,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 11:23:08,167] [INFO] Task started: Prodigal
[2023-06-19 11:23:08,168] [INFO] Running command: gunzip -c /var/lib/cwl/stge295e034-65cd-4138-85a1-fe568fb075ec/GCA_018399755.1_ASM1839975v1_genomic.fna.gz | prodigal -d GCA_018399755.1_ASM1839975v1_genomic.fna/cds.fna -a GCA_018399755.1_ASM1839975v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 11:23:09,961] [INFO] Task succeeded: Prodigal
[2023-06-19 11:23:09,962] [INFO] Task started: HMMsearch
[2023-06-19 11:23:09,962] [INFO] Running command: hmmsearch --tblout GCA_018399755.1_ASM1839975v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg594601f0-af39-442c-895e-c6651bb078c4/dqc_reference/reference_markers.hmm GCA_018399755.1_ASM1839975v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 11:23:10,199] [INFO] Task succeeded: HMMsearch
[2023-06-19 11:23:10,201] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge295e034-65cd-4138-85a1-fe568fb075ec/GCA_018399755.1_ASM1839975v1_genomic.fna.gz]
[2023-06-19 11:23:10,217] [INFO] Query marker FASTA was written to GCA_018399755.1_ASM1839975v1_genomic.fna/markers.fasta
[2023-06-19 11:23:10,218] [INFO] Task started: Blastn
[2023-06-19 11:23:10,218] [INFO] Running command: blastn -query GCA_018399755.1_ASM1839975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg594601f0-af39-442c-895e-c6651bb078c4/dqc_reference/reference_markers.fasta -out GCA_018399755.1_ASM1839975v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:23:10,813] [INFO] Task succeeded: Blastn
[2023-06-19 11:23:10,817] [INFO] Selected 16 target genomes.
[2023-06-19 11:23:10,818] [INFO] Target genome list was writen to GCA_018399755.1_ASM1839975v1_genomic.fna/target_genomes.txt
[2023-06-19 11:23:10,820] [INFO] Task started: fastANI
[2023-06-19 11:23:10,820] [INFO] Running command: fastANI --query /var/lib/cwl/stge295e034-65cd-4138-85a1-fe568fb075ec/GCA_018399755.1_ASM1839975v1_genomic.fna.gz --refList GCA_018399755.1_ASM1839975v1_genomic.fna/target_genomes.txt --output GCA_018399755.1_ASM1839975v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 11:23:17,506] [INFO] Task succeeded: fastANI
[2023-06-19 11:23:17,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg594601f0-af39-442c-895e-c6651bb078c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 11:23:17,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg594601f0-af39-442c-895e-c6651bb078c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 11:23:17,509] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 11:23:17,509] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 11:23:17,509] [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
--------------------------------------------------------------------------------
[2023-06-19 11:23:17,511] [INFO] DFAST Taxonomy check result was written to GCA_018399755.1_ASM1839975v1_genomic.fna/tc_result.tsv
[2023-06-19 11:23:17,511] [INFO] ===== Taxonomy check completed =====
[2023-06-19 11:23:17,512] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 11:23:17,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg594601f0-af39-442c-895e-c6651bb078c4/dqc_reference/checkm_data
[2023-06-19 11:23:17,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 11:23:17,535] [INFO] Task started: CheckM
[2023-06-19 11:23:17,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018399755.1_ASM1839975v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018399755.1_ASM1839975v1_genomic.fna/checkm_input GCA_018399755.1_ASM1839975v1_genomic.fna/checkm_result
[2023-06-19 11:23:32,379] [INFO] Task succeeded: CheckM
[2023-06-19 11:23:32,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 11:23:32,403] [INFO] ===== Completeness check finished =====
[2023-06-19 11:23:32,403] [INFO] ===== Start GTDB Search =====
[2023-06-19 11:23:32,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018399755.1_ASM1839975v1_genomic.fna/markers.fasta)
[2023-06-19 11:23:32,404] [INFO] Task started: Blastn
[2023-06-19 11:23:32,405] [INFO] Running command: blastn -query GCA_018399755.1_ASM1839975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg594601f0-af39-442c-895e-c6651bb078c4/dqc_reference/reference_markers_gtdb.fasta -out GCA_018399755.1_ASM1839975v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:23:33,257] [INFO] Task succeeded: Blastn
[2023-06-19 11:23:33,261] [INFO] Selected 17 target genomes.
[2023-06-19 11:23:33,261] [INFO] Target genome list was writen to GCA_018399755.1_ASM1839975v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 11:23:33,345] [INFO] Task started: fastANI
[2023-06-19 11:23:33,346] [INFO] Running command: fastANI --query /var/lib/cwl/stge295e034-65cd-4138-85a1-fe568fb075ec/GCA_018399755.1_ASM1839975v1_genomic.fna.gz --refList GCA_018399755.1_ASM1839975v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018399755.1_ASM1839975v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 11:23:37,741] [INFO] Task succeeded: fastANI
[2023-06-19 11:23:37,751] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 11:23:37,752] [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_018399755.1	s__Zrk29 sp018399755	100.0	366	371	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA5603;g__Zrk29	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013745115.1	s__Zrk29 sp013745115	78.0313	142	371	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA5603;g__Zrk29	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345425.1	s__UBA2289 sp002345425	77.3434	77	371	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA5603;g__UBA2289	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002419505.1	s__UBA2289 sp002419505	77.08	67	371	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA5603;g__UBA2289	95.0	99.26	99.26	0.88	0.88	2	-
GCA_002084435.1	s__4572-104 sp002084435	76.6966	51	371	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA5603;g__4572-104	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345505.1	s__UBA2289 sp002345505	76.6144	63	371	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA5603;g__UBA2289	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 11:23:37,754] [INFO] GTDB search result was written to GCA_018399755.1_ASM1839975v1_genomic.fna/result_gtdb.tsv
[2023-06-19 11:23:37,754] [INFO] ===== GTDB Search completed =====
[2023-06-19 11:23:37,757] [INFO] DFAST_QC result json was written to GCA_018399755.1_ASM1839975v1_genomic.fna/dqc_result.json
[2023-06-19 11:23:37,757] [INFO] DFAST_QC completed!
[2023-06-19 11:23:37,758] [INFO] Total running time: 0h0m31s