[2023-06-13 00:09:46,593] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:09:46,596] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:09:46,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg00f544c0-c470-4f48-a218-4f6a01470452/dqc_reference
[2023-06-13 00:09:49,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:09:49,337] [INFO] Task started: Prodigal
[2023-06-13 00:09:49,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg68843565-2b78-41e2-b006-264a19eca2c3/GCA_022792335.1_ASM2279233v1_genomic.fna.gz | prodigal -d GCA_022792335.1_ASM2279233v1_genomic.fna/cds.fna -a GCA_022792335.1_ASM2279233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:09:55,685] [INFO] Task succeeded: Prodigal
[2023-06-13 00:09:55,686] [INFO] Task started: HMMsearch
[2023-06-13 00:09:55,686] [INFO] Running command: hmmsearch --tblout GCA_022792335.1_ASM2279233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00f544c0-c470-4f48-a218-4f6a01470452/dqc_reference/reference_markers.hmm GCA_022792335.1_ASM2279233v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:09:55,927] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:09:55,928] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg68843565-2b78-41e2-b006-264a19eca2c3/GCA_022792335.1_ASM2279233v1_genomic.fna.gz]
[2023-06-13 00:09:55,964] [INFO] Query marker FASTA was written to GCA_022792335.1_ASM2279233v1_genomic.fna/markers.fasta
[2023-06-13 00:09:55,965] [INFO] Task started: Blastn
[2023-06-13 00:09:55,965] [INFO] Running command: blastn -query GCA_022792335.1_ASM2279233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00f544c0-c470-4f48-a218-4f6a01470452/dqc_reference/reference_markers.fasta -out GCA_022792335.1_ASM2279233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:09:56,460] [INFO] Task succeeded: Blastn
[2023-06-13 00:09:56,465] [INFO] Selected 22 target genomes.
[2023-06-13 00:09:56,466] [INFO] Target genome list was writen to GCA_022792335.1_ASM2279233v1_genomic.fna/target_genomes.txt
[2023-06-13 00:09:56,468] [INFO] Task started: fastANI
[2023-06-13 00:09:56,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg68843565-2b78-41e2-b006-264a19eca2c3/GCA_022792335.1_ASM2279233v1_genomic.fna.gz --refList GCA_022792335.1_ASM2279233v1_genomic.fna/target_genomes.txt --output GCA_022792335.1_ASM2279233v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:10:07,788] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:07,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00f544c0-c470-4f48-a218-4f6a01470452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:10:07,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00f544c0-c470-4f48-a218-4f6a01470452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:10:07,796] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:10:07,796] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 00:10:07,796] [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
Qiania dongpingensis	strain=NSJ-38	GCA_014337195.1	2763669	2763669	type	True	77.2662	162	858	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:10:07,799] [INFO] DFAST Taxonomy check result was written to GCA_022792335.1_ASM2279233v1_genomic.fna/tc_result.tsv
[2023-06-13 00:10:07,799] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:10:07,800] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:10:07,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00f544c0-c470-4f48-a218-4f6a01470452/dqc_reference/checkm_data
[2023-06-13 00:10:07,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:10:07,835] [INFO] Task started: CheckM
[2023-06-13 00:10:07,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022792335.1_ASM2279233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022792335.1_ASM2279233v1_genomic.fna/checkm_input GCA_022792335.1_ASM2279233v1_genomic.fna/checkm_result
[2023-06-13 00:10:33,461] [INFO] Task succeeded: CheckM
[2023-06-13 00:10:33,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:10:33,490] [INFO] ===== Completeness check finished =====
[2023-06-13 00:10:33,492] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:10:33,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022792335.1_ASM2279233v1_genomic.fna/markers.fasta)
[2023-06-13 00:10:33,493] [INFO] Task started: Blastn
[2023-06-13 00:10:33,493] [INFO] Running command: blastn -query GCA_022792335.1_ASM2279233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00f544c0-c470-4f48-a218-4f6a01470452/dqc_reference/reference_markers_gtdb.fasta -out GCA_022792335.1_ASM2279233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:10:33,955] [INFO] Task succeeded: Blastn
[2023-06-13 00:10:33,959] [INFO] Selected 17 target genomes.
[2023-06-13 00:10:33,959] [INFO] Target genome list was writen to GCA_022792335.1_ASM2279233v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:10:33,996] [INFO] Task started: fastANI
[2023-06-13 00:10:33,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg68843565-2b78-41e2-b006-264a19eca2c3/GCA_022792335.1_ASM2279233v1_genomic.fna.gz --refList GCA_022792335.1_ASM2279233v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022792335.1_ASM2279233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:10:42,361] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:42,369] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 00:10:42,369] [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_910588815.1	s__Paralachnospira sp910588815	79.6212	411	858	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587905.1	s__Paralachnospira sp910587905	79.5053	349	858	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904379015.1	s__Paralachnospira caecorum	77.5031	162	858	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	99.98	99.98	0.92	0.92	2	-
GCA_014337195.1	s__Paralachnospira sp014337195	77.2663	162	858	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363445.1	s__Paralachnospira sp902363445	77.262	177	858	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 00:10:42,373] [INFO] GTDB search result was written to GCA_022792335.1_ASM2279233v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:10:42,373] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:10:42,377] [INFO] DFAST_QC result json was written to GCA_022792335.1_ASM2279233v1_genomic.fna/dqc_result.json
[2023-06-13 00:10:42,378] [INFO] DFAST_QC completed!
[2023-06-13 00:10:42,378] [INFO] Total running time: 0h0m56s