[2023-06-30 12:00:10,696] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:00:10,699] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:00:10,699] [INFO] DQC Reference Directory: /var/lib/cwl/stgb86124ee-4aee-4c12-bddd-21a45b879fe6/dqc_reference
[2023-06-30 12:00:11,905] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:00:11,906] [INFO] Task started: Prodigal
[2023-06-30 12:00:11,906] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcf68fb6-5157-4547-8f64-310b243963f4/GCA_024405015.1_ASM2440501v1_genomic.fna.gz | prodigal -d GCA_024405015.1_ASM2440501v1_genomic.fna/cds.fna -a GCA_024405015.1_ASM2440501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:00:17,738] [INFO] Task succeeded: Prodigal
[2023-06-30 12:00:17,738] [INFO] Task started: HMMsearch
[2023-06-30 12:00:17,739] [INFO] Running command: hmmsearch --tblout GCA_024405015.1_ASM2440501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb86124ee-4aee-4c12-bddd-21a45b879fe6/dqc_reference/reference_markers.hmm GCA_024405015.1_ASM2440501v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:00:17,963] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:00:17,965] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbcf68fb6-5157-4547-8f64-310b243963f4/GCA_024405015.1_ASM2440501v1_genomic.fna.gz]
[2023-06-30 12:00:17,992] [INFO] Query marker FASTA was written to GCA_024405015.1_ASM2440501v1_genomic.fna/markers.fasta
[2023-06-30 12:00:17,993] [INFO] Task started: Blastn
[2023-06-30 12:00:17,993] [INFO] Running command: blastn -query GCA_024405015.1_ASM2440501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb86124ee-4aee-4c12-bddd-21a45b879fe6/dqc_reference/reference_markers.fasta -out GCA_024405015.1_ASM2440501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:00:18,563] [INFO] Task succeeded: Blastn
[2023-06-30 12:00:18,567] [INFO] Selected 8 target genomes.
[2023-06-30 12:00:18,568] [INFO] Target genome list was writen to GCA_024405015.1_ASM2440501v1_genomic.fna/target_genomes.txt
[2023-06-30 12:00:18,571] [INFO] Task started: fastANI
[2023-06-30 12:00:18,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcf68fb6-5157-4547-8f64-310b243963f4/GCA_024405015.1_ASM2440501v1_genomic.fna.gz --refList GCA_024405015.1_ASM2440501v1_genomic.fna/target_genomes.txt --output GCA_024405015.1_ASM2440501v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:00:22,568] [INFO] Task succeeded: fastANI
[2023-06-30 12:00:22,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb86124ee-4aee-4c12-bddd-21a45b879fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:00:22,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb86124ee-4aee-4c12-bddd-21a45b879fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:00:22,570] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:00:22,570] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 12:00:22,571] [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
--------------------------------------------------------------------------------
[2023-06-30 12:00:22,572] [INFO] DFAST Taxonomy check result was written to GCA_024405015.1_ASM2440501v1_genomic.fna/tc_result.tsv
[2023-06-30 12:00:22,573] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:00:22,573] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:00:22,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb86124ee-4aee-4c12-bddd-21a45b879fe6/dqc_reference/checkm_data
[2023-06-30 12:00:22,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:00:22,601] [INFO] Task started: CheckM
[2023-06-30 12:00:22,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024405015.1_ASM2440501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024405015.1_ASM2440501v1_genomic.fna/checkm_input GCA_024405015.1_ASM2440501v1_genomic.fna/checkm_result
[2023-06-30 12:00:47,638] [INFO] Task succeeded: CheckM
[2023-06-30 12:00:47,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:00:47,665] [INFO] ===== Completeness check finished =====
[2023-06-30 12:00:47,666] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:00:47,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024405015.1_ASM2440501v1_genomic.fna/markers.fasta)
[2023-06-30 12:00:47,667] [INFO] Task started: Blastn
[2023-06-30 12:00:47,667] [INFO] Running command: blastn -query GCA_024405015.1_ASM2440501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb86124ee-4aee-4c12-bddd-21a45b879fe6/dqc_reference/reference_markers_gtdb.fasta -out GCA_024405015.1_ASM2440501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:00:48,514] [INFO] Task succeeded: Blastn
[2023-06-30 12:00:48,519] [INFO] Selected 13 target genomes.
[2023-06-30 12:00:48,520] [INFO] Target genome list was writen to GCA_024405015.1_ASM2440501v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:00:48,528] [INFO] Task started: fastANI
[2023-06-30 12:00:48,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcf68fb6-5157-4547-8f64-310b243963f4/GCA_024405015.1_ASM2440501v1_genomic.fna.gz --refList GCA_024405015.1_ASM2440501v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024405015.1_ASM2440501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:00:52,485] [INFO] Task succeeded: fastANI
[2023-06-30 12:00:52,494] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 12:00:52,495] [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_017632495.1	s__UBA9732 sp017632495	78.6172	113	650	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003456855.1	s__UBA9732 sp003456855	78.3531	133	650	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470995.1	s__UBA9732 sp017470995	78.1934	138	650	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781545.1	s__UBA9732 sp902781545	78.129	141	650	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	96.71	95.62	0.84	0.79	12	-
GCA_900321635.1	s__UBA9732 sp900321635	78.0836	140	650	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902796335.1	s__UBA9732 sp902796335	77.7783	114	650	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017475725.1	s__UBA9732 sp017475725	77.7207	96	650	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962865.1	s__UBA9732 sp017962865	77.598	91	650	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017618315.1	s__UBA9732 sp017618315	77.3252	92	650	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	96.94	96.94	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-30 12:00:52,497] [INFO] GTDB search result was written to GCA_024405015.1_ASM2440501v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:00:52,498] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:00:52,501] [INFO] DFAST_QC result json was written to GCA_024405015.1_ASM2440501v1_genomic.fna/dqc_result.json
[2023-06-30 12:00:52,501] [INFO] DFAST_QC completed!
[2023-06-30 12:00:52,501] [INFO] Total running time: 0h0m42s