[2023-06-28 15:26:04,867] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:26:04,892] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:26:04,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d9f4863-c9d8-439a-aee5-454133295ad0/dqc_reference
[2023-06-28 15:26:06,385] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:26:06,386] [INFO] Task started: Prodigal
[2023-06-28 15:26:06,386] [INFO] Running command: gunzip -c /var/lib/cwl/stg890d44c6-e051-4c0f-8baf-a1dbc4c482b8/GCA_017552705.1_ASM1755270v1_genomic.fna.gz | prodigal -d GCA_017552705.1_ASM1755270v1_genomic.fna/cds.fna -a GCA_017552705.1_ASM1755270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:26:24,344] [INFO] Task succeeded: Prodigal
[2023-06-28 15:26:24,344] [INFO] Task started: HMMsearch
[2023-06-28 15:26:24,345] [INFO] Running command: hmmsearch --tblout GCA_017552705.1_ASM1755270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d9f4863-c9d8-439a-aee5-454133295ad0/dqc_reference/reference_markers.hmm GCA_017552705.1_ASM1755270v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:26:24,620] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:26:24,622] [INFO] Found 6/6 markers.
[2023-06-28 15:26:24,665] [INFO] Query marker FASTA was written to GCA_017552705.1_ASM1755270v1_genomic.fna/markers.fasta
[2023-06-28 15:26:24,666] [INFO] Task started: Blastn
[2023-06-28 15:26:24,666] [INFO] Running command: blastn -query GCA_017552705.1_ASM1755270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d9f4863-c9d8-439a-aee5-454133295ad0/dqc_reference/reference_markers.fasta -out GCA_017552705.1_ASM1755270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:26:25,270] [INFO] Task succeeded: Blastn
[2023-06-28 15:26:25,275] [INFO] Selected 26 target genomes.
[2023-06-28 15:26:25,275] [INFO] Target genome list was writen to GCA_017552705.1_ASM1755270v1_genomic.fna/target_genomes.txt
[2023-06-28 15:26:25,281] [INFO] Task started: fastANI
[2023-06-28 15:26:25,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg890d44c6-e051-4c0f-8baf-a1dbc4c482b8/GCA_017552705.1_ASM1755270v1_genomic.fna.gz --refList GCA_017552705.1_ASM1755270v1_genomic.fna/target_genomes.txt --output GCA_017552705.1_ASM1755270v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:26:45,693] [INFO] Task succeeded: fastANI
[2023-06-28 15:26:45,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d9f4863-c9d8-439a-aee5-454133295ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:26:45,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d9f4863-c9d8-439a-aee5-454133295ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:26:45,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:26:45,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 15:26:45,696] [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 15:26:45,699] [INFO] DFAST Taxonomy check result was written to GCA_017552705.1_ASM1755270v1_genomic.fna/tc_result.tsv
[2023-06-28 15:26:45,699] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:26:45,699] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:26:45,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d9f4863-c9d8-439a-aee5-454133295ad0/dqc_reference/checkm_data
[2023-06-28 15:26:45,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:26:45,750] [INFO] Task started: CheckM
[2023-06-28 15:26:45,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017552705.1_ASM1755270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017552705.1_ASM1755270v1_genomic.fna/checkm_input GCA_017552705.1_ASM1755270v1_genomic.fna/checkm_result
[2023-06-28 15:27:41,712] [INFO] Task succeeded: CheckM
[2023-06-28 15:27:41,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.54%
Contamintation: 6.48%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:27:41,740] [INFO] ===== Completeness check finished =====
[2023-06-28 15:27:41,740] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:27:41,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017552705.1_ASM1755270v1_genomic.fna/markers.fasta)
[2023-06-28 15:27:41,741] [INFO] Task started: Blastn
[2023-06-28 15:27:41,741] [INFO] Running command: blastn -query GCA_017552705.1_ASM1755270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d9f4863-c9d8-439a-aee5-454133295ad0/dqc_reference/reference_markers_gtdb.fasta -out GCA_017552705.1_ASM1755270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:27:42,552] [INFO] Task succeeded: Blastn
[2023-06-28 15:27:42,556] [INFO] Selected 16 target genomes.
[2023-06-28 15:27:42,556] [INFO] Target genome list was writen to GCA_017552705.1_ASM1755270v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:27:42,564] [INFO] Task started: fastANI
[2023-06-28 15:27:42,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg890d44c6-e051-4c0f-8baf-a1dbc4c482b8/GCA_017552705.1_ASM1755270v1_genomic.fna.gz --refList GCA_017552705.1_ASM1755270v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017552705.1_ASM1755270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:27:51,236] [INFO] Task succeeded: fastANI
[2023-06-28 15:27:51,247] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 15:27:51,247] [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_017552705.1	s__UBA1715 sp017552705	100.0	885	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017618935.1	s__UBA1715 sp017618935	84.1961	314	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	95.58	95.58	0.68	0.68	2	-
GCA_002371705.1	s__UBA1715 sp002371705	83.8162	573	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	97.12	96.45	0.83	0.72	7	-
GCA_017642535.1	s__UBA1715 sp017642535	83.0532	390	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017516865.1	s__UBA1715 sp017516865	81.7097	367	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002317135.1	s__UBA1715 sp002317135	78.0031	176	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1715;g__UBA1715	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:27:51,250] [INFO] GTDB search result was written to GCA_017552705.1_ASM1755270v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:27:51,251] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:27:51,266] [INFO] DFAST_QC result json was written to GCA_017552705.1_ASM1755270v1_genomic.fna/dqc_result.json
[2023-06-28 15:27:51,266] [INFO] DFAST_QC completed!
[2023-06-28 15:27:51,266] [INFO] Total running time: 0h1m46s