[2023-06-28 12:03:02,695] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:03:02,699] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:03:02,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg9776e379-e550-43e2-9eba-09754c5617e8/dqc_reference
[2023-06-28 12:03:04,017] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:03:04,018] [INFO] Task started: Prodigal
[2023-06-28 12:03:04,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg097ba7c5-df79-481d-a758-462558985305/GCA_020718585.1_ASM2071858v1_genomic.fna.gz | prodigal -d GCA_020718585.1_ASM2071858v1_genomic.fna/cds.fna -a GCA_020718585.1_ASM2071858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:03:19,049] [INFO] Task succeeded: Prodigal
[2023-06-28 12:03:19,049] [INFO] Task started: HMMsearch
[2023-06-28 12:03:19,050] [INFO] Running command: hmmsearch --tblout GCA_020718585.1_ASM2071858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9776e379-e550-43e2-9eba-09754c5617e8/dqc_reference/reference_markers.hmm GCA_020718585.1_ASM2071858v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:03:19,272] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:03:19,274] [INFO] Found 6/6 markers.
[2023-06-28 12:03:19,310] [INFO] Query marker FASTA was written to GCA_020718585.1_ASM2071858v1_genomic.fna/markers.fasta
[2023-06-28 12:03:19,311] [INFO] Task started: Blastn
[2023-06-28 12:03:19,311] [INFO] Running command: blastn -query GCA_020718585.1_ASM2071858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9776e379-e550-43e2-9eba-09754c5617e8/dqc_reference/reference_markers.fasta -out GCA_020718585.1_ASM2071858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:19,955] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:19,959] [INFO] Selected 22 target genomes.
[2023-06-28 12:03:19,960] [INFO] Target genome list was writen to GCA_020718585.1_ASM2071858v1_genomic.fna/target_genomes.txt
[2023-06-28 12:03:19,972] [INFO] Task started: fastANI
[2023-06-28 12:03:19,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg097ba7c5-df79-481d-a758-462558985305/GCA_020718585.1_ASM2071858v1_genomic.fna.gz --refList GCA_020718585.1_ASM2071858v1_genomic.fna/target_genomes.txt --output GCA_020718585.1_ASM2071858v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:03:36,232] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:36,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9776e379-e550-43e2-9eba-09754c5617e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:03:36,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9776e379-e550-43e2-9eba-09754c5617e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:03:36,239] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:03:36,239] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:03:36,239] [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
Terrimicrobium sacchariphilum	strain=NM-5	GCA_001613545.1	690879	690879	type	True	76.2177	84	684	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	74.8656	53	684	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	74.8059	50	684	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:03:36,241] [INFO] DFAST Taxonomy check result was written to GCA_020718585.1_ASM2071858v1_genomic.fna/tc_result.tsv
[2023-06-28 12:03:36,242] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:03:36,242] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:03:36,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9776e379-e550-43e2-9eba-09754c5617e8/dqc_reference/checkm_data
[2023-06-28 12:03:36,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:03:36,282] [INFO] Task started: CheckM
[2023-06-28 12:03:36,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020718585.1_ASM2071858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020718585.1_ASM2071858v1_genomic.fna/checkm_input GCA_020718585.1_ASM2071858v1_genomic.fna/checkm_result
[2023-06-28 12:04:18,833] [INFO] Task succeeded: CheckM
[2023-06-28 12:04:18,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:04:18,862] [INFO] ===== Completeness check finished =====
[2023-06-28 12:04:18,862] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:04:18,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020718585.1_ASM2071858v1_genomic.fna/markers.fasta)
[2023-06-28 12:04:18,863] [INFO] Task started: Blastn
[2023-06-28 12:04:18,863] [INFO] Running command: blastn -query GCA_020718585.1_ASM2071858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9776e379-e550-43e2-9eba-09754c5617e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_020718585.1_ASM2071858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:19,864] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:19,869] [INFO] Selected 18 target genomes.
[2023-06-28 12:04:19,869] [INFO] Target genome list was writen to GCA_020718585.1_ASM2071858v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:04:19,910] [INFO] Task started: fastANI
[2023-06-28 12:04:19,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg097ba7c5-df79-481d-a758-462558985305/GCA_020718585.1_ASM2071858v1_genomic.fna.gz --refList GCA_020718585.1_ASM2071858v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020718585.1_ASM2071858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:04:30,476] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:30,489] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:04:30,489] [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_007280915.1	s__QYQL01 sp007280915	78.8674	263	684	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__QYQL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970255.1	s__UBA967 sp018970255	77.7331	127	684	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402345.1	s__UBA967 sp018402345	76.8927	114	684	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879575.1	s__QYQL01 sp014879575	76.748	148	684	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__QYQL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655545.1	s__JAATET01 sp015655545	76.4455	85	684	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JAATET01;g__JAATET01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002396485.1	s__UBA967 sp002396485	76.2722	71	684	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885995.1	s__VFJQ01 sp009885995	76.219	73	684	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__VFJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882875.1	s__SXWH01 sp903882875	76.1526	68	684	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	99.98	99.97	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2023-06-28 12:04:30,491] [INFO] GTDB search result was written to GCA_020718585.1_ASM2071858v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:04:30,492] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:04:30,494] [INFO] DFAST_QC result json was written to GCA_020718585.1_ASM2071858v1_genomic.fna/dqc_result.json
[2023-06-28 12:04:30,494] [INFO] DFAST_QC completed!
[2023-06-28 12:04:30,495] [INFO] Total running time: 0h1m28s