[2023-06-29 12:45:35,337] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:45:35,339] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:45:35,340] [INFO] DQC Reference Directory: /var/lib/cwl/stgb541c2b0-3be4-4c99-80fa-b9e01cfdf7c7/dqc_reference
[2023-06-29 12:45:36,519] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:45:36,520] [INFO] Task started: Prodigal
[2023-06-29 12:45:36,520] [INFO] Running command: gunzip -c /var/lib/cwl/stg3291f33d-ef1f-4309-9eb7-f345c432c131/GCA_023438065.1_ASM2343806v1_genomic.fna.gz | prodigal -d GCA_023438065.1_ASM2343806v1_genomic.fna/cds.fna -a GCA_023438065.1_ASM2343806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:45:44,429] [INFO] Task succeeded: Prodigal
[2023-06-29 12:45:44,430] [INFO] Task started: HMMsearch
[2023-06-29 12:45:44,430] [INFO] Running command: hmmsearch --tblout GCA_023438065.1_ASM2343806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb541c2b0-3be4-4c99-80fa-b9e01cfdf7c7/dqc_reference/reference_markers.hmm GCA_023438065.1_ASM2343806v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:45:44,678] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:45:44,680] [INFO] Found 6/6 markers.
[2023-06-29 12:45:44,724] [INFO] Query marker FASTA was written to GCA_023438065.1_ASM2343806v1_genomic.fna/markers.fasta
[2023-06-29 12:45:44,724] [INFO] Task started: Blastn
[2023-06-29 12:45:44,724] [INFO] Running command: blastn -query GCA_023438065.1_ASM2343806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb541c2b0-3be4-4c99-80fa-b9e01cfdf7c7/dqc_reference/reference_markers.fasta -out GCA_023438065.1_ASM2343806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:45:45,377] [INFO] Task succeeded: Blastn
[2023-06-29 12:45:45,383] [INFO] Selected 34 target genomes.
[2023-06-29 12:45:45,383] [INFO] Target genome list was writen to GCA_023438065.1_ASM2343806v1_genomic.fna/target_genomes.txt
[2023-06-29 12:45:45,386] [INFO] Task started: fastANI
[2023-06-29 12:45:45,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg3291f33d-ef1f-4309-9eb7-f345c432c131/GCA_023438065.1_ASM2343806v1_genomic.fna.gz --refList GCA_023438065.1_ASM2343806v1_genomic.fna/target_genomes.txt --output GCA_023438065.1_ASM2343806v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:46:09,784] [INFO] Task succeeded: fastANI
[2023-06-29 12:46:09,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb541c2b0-3be4-4c99-80fa-b9e01cfdf7c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:46:09,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb541c2b0-3be4-4c99-80fa-b9e01cfdf7c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:46:09,791] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:46:09,792] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:46:09,792] [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
Treponema zuelzerae	strain=DSM 1903	GCA_021021555.1	156	156	type	True	77.5902	185	1081	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.7384	100	1081	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:46:09,794] [INFO] DFAST Taxonomy check result was written to GCA_023438065.1_ASM2343806v1_genomic.fna/tc_result.tsv
[2023-06-29 12:46:09,795] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:46:09,795] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:46:09,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb541c2b0-3be4-4c99-80fa-b9e01cfdf7c7/dqc_reference/checkm_data
[2023-06-29 12:46:09,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:46:09,834] [INFO] Task started: CheckM
[2023-06-29 12:46:09,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023438065.1_ASM2343806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023438065.1_ASM2343806v1_genomic.fna/checkm_input GCA_023438065.1_ASM2343806v1_genomic.fna/checkm_result
[2023-06-29 12:46:37,658] [INFO] Task succeeded: CheckM
[2023-06-29 12:46:37,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:46:37,684] [INFO] ===== Completeness check finished =====
[2023-06-29 12:46:37,685] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:46:37,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023438065.1_ASM2343806v1_genomic.fna/markers.fasta)
[2023-06-29 12:46:37,685] [INFO] Task started: Blastn
[2023-06-29 12:46:37,686] [INFO] Running command: blastn -query GCA_023438065.1_ASM2343806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb541c2b0-3be4-4c99-80fa-b9e01cfdf7c7/dqc_reference/reference_markers_gtdb.fasta -out GCA_023438065.1_ASM2343806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:46:38,691] [INFO] Task succeeded: Blastn
[2023-06-29 12:46:38,696] [INFO] Selected 28 target genomes.
[2023-06-29 12:46:38,696] [INFO] Target genome list was writen to GCA_023438065.1_ASM2343806v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:46:38,710] [INFO] Task started: fastANI
[2023-06-29 12:46:38,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg3291f33d-ef1f-4309-9eb7-f345c432c131/GCA_023438065.1_ASM2343806v1_genomic.fna.gz --refList GCA_023438065.1_ASM2343806v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023438065.1_ASM2343806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:46:54,931] [INFO] Task succeeded: fastANI
[2023-06-29 12:46:54,943] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:46:54,943] [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_001604405.1	s__Spiro-10 sp001604405	79.2897	350	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Spiro-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003245785.1	s__Spiro-10 sp003245785	78.3179	240	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Spiro-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003246765.1	s__Spiro-10 sp003246765	78.0414	190	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Spiro-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003246335.1	s__Spiro-10 sp003246335	77.972	244	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Spiro-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252395.1	s__Spiro-10 sp003252395	77.8919	211	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Spiro-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003245635.1	s__SZUA-426 sp003245635	77.3879	95	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__SZUA-426	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938205.1	s__Spiro-10 sp016938205	77.2933	128	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Spiro-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794765.1	s__JAEUJG01 sp016794765	76.9305	92	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__JAEUJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262985.1	s__JAFGNN01 sp018262985	76.8373	108	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAFGNN01	95.0	98.32	98.32	0.96	0.96	2	-
GCA_002070025.1	s__DUOS01 sp002070025	76.8311	100	1081	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__DUOS01	95.0	98.94	98.94	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-29 12:46:54,945] [INFO] GTDB search result was written to GCA_023438065.1_ASM2343806v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:46:54,946] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:46:54,949] [INFO] DFAST_QC result json was written to GCA_023438065.1_ASM2343806v1_genomic.fna/dqc_result.json
[2023-06-29 12:46:54,949] [INFO] DFAST_QC completed!
[2023-06-29 12:46:54,949] [INFO] Total running time: 0h1m20s