[2023-06-29 15:55:41,174] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:55:41,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:55:41,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgebdebeef-5c92-4b91-9224-93632f93cdb5/dqc_reference
[2023-06-29 15:55:42,376] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:55:42,377] [INFO] Task started: Prodigal
[2023-06-29 15:55:42,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg12e2d195-6e5a-4a92-af49-7742291e23ea/GCA_021205305.1_ASM2120530v1_genomic.fna.gz | prodigal -d GCA_021205305.1_ASM2120530v1_genomic.fna/cds.fna -a GCA_021205305.1_ASM2120530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:55:49,485] [INFO] Task succeeded: Prodigal
[2023-06-29 15:55:49,486] [INFO] Task started: HMMsearch
[2023-06-29 15:55:49,486] [INFO] Running command: hmmsearch --tblout GCA_021205305.1_ASM2120530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebdebeef-5c92-4b91-9224-93632f93cdb5/dqc_reference/reference_markers.hmm GCA_021205305.1_ASM2120530v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:55:49,757] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:55:49,758] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg12e2d195-6e5a-4a92-af49-7742291e23ea/GCA_021205305.1_ASM2120530v1_genomic.fna.gz]
[2023-06-29 15:55:49,789] [INFO] Query marker FASTA was written to GCA_021205305.1_ASM2120530v1_genomic.fna/markers.fasta
[2023-06-29 15:55:49,790] [INFO] Task started: Blastn
[2023-06-29 15:55:49,790] [INFO] Running command: blastn -query GCA_021205305.1_ASM2120530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebdebeef-5c92-4b91-9224-93632f93cdb5/dqc_reference/reference_markers.fasta -out GCA_021205305.1_ASM2120530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:55:50,442] [INFO] Task succeeded: Blastn
[2023-06-29 15:55:50,446] [INFO] Selected 23 target genomes.
[2023-06-29 15:55:50,447] [INFO] Target genome list was writen to GCA_021205305.1_ASM2120530v1_genomic.fna/target_genomes.txt
[2023-06-29 15:55:50,449] [INFO] Task started: fastANI
[2023-06-29 15:55:50,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg12e2d195-6e5a-4a92-af49-7742291e23ea/GCA_021205305.1_ASM2120530v1_genomic.fna.gz --refList GCA_021205305.1_ASM2120530v1_genomic.fna/target_genomes.txt --output GCA_021205305.1_ASM2120530v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:56:02,746] [INFO] Task succeeded: fastANI
[2023-06-29 15:56:02,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebdebeef-5c92-4b91-9224-93632f93cdb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:56:02,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebdebeef-5c92-4b91-9224-93632f93cdb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:56:02,755] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:56:02,756] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:56:02,756] [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
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.9308	82	944	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.9035	84	944	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:56:02,758] [INFO] DFAST Taxonomy check result was written to GCA_021205305.1_ASM2120530v1_genomic.fna/tc_result.tsv
[2023-06-29 15:56:02,759] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:56:02,759] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:56:02,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebdebeef-5c92-4b91-9224-93632f93cdb5/dqc_reference/checkm_data
[2023-06-29 15:56:02,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:56:02,798] [INFO] Task started: CheckM
[2023-06-29 15:56:02,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021205305.1_ASM2120530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021205305.1_ASM2120530v1_genomic.fna/checkm_input GCA_021205305.1_ASM2120530v1_genomic.fna/checkm_result
[2023-06-29 15:56:30,598] [INFO] Task succeeded: CheckM
[2023-06-29 15:56:30,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:56:30,622] [INFO] ===== Completeness check finished =====
[2023-06-29 15:56:30,623] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:56:30,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021205305.1_ASM2120530v1_genomic.fna/markers.fasta)
[2023-06-29 15:56:30,624] [INFO] Task started: Blastn
[2023-06-29 15:56:30,624] [INFO] Running command: blastn -query GCA_021205305.1_ASM2120530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebdebeef-5c92-4b91-9224-93632f93cdb5/dqc_reference/reference_markers_gtdb.fasta -out GCA_021205305.1_ASM2120530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:56:31,722] [INFO] Task succeeded: Blastn
[2023-06-29 15:56:31,727] [INFO] Selected 24 target genomes.
[2023-06-29 15:56:31,727] [INFO] Target genome list was writen to GCA_021205305.1_ASM2120530v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:56:31,731] [INFO] Task started: fastANI
[2023-06-29 15:56:31,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg12e2d195-6e5a-4a92-af49-7742291e23ea/GCA_021205305.1_ASM2120530v1_genomic.fna.gz --refList GCA_021205305.1_ASM2120530v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021205305.1_ASM2120530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:56:44,152] [INFO] Task succeeded: fastANI
[2023-06-29 15:56:44,163] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:56:44,163] [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_001941045.1	s__Choladocola sp001941045	78.1458	87	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491565.1	s__Choladousia sp002491565	77.3706	114	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363135.1	s__Choladousia sp902363135	77.0582	121	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.66	98.47	0.96	0.95	4	-
GCA_905201705.1	s__Marvinbryantia sp900550755	77.0508	89	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.85	99.71	0.93	0.91	3	-
GCA_902363665.1	s__Choladousia sp902363665	76.9643	118	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	97.59	97.59	0.93	0.93	2	-
GCF_000173815.1	s__Marvinbryantia formatexigens	76.9032	84	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.98	99.98	0.99	0.99	3	-
GCA_018712785.1	s__Choladousia intestinavium	76.5102	67	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.61	98.61	0.86	0.86	2	-
GCA_902783665.1	s__Choladousia sp902783665	76.4241	50	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757145.1	s__Choladousia sp900757145	76.3932	60	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	99.16	99.16	0.96	0.96	2	-
GCA_910584945.1	s__Choladocola sp910584945	75.8629	55	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:56:44,180] [INFO] GTDB search result was written to GCA_021205305.1_ASM2120530v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:56:44,181] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:56:44,185] [INFO] DFAST_QC result json was written to GCA_021205305.1_ASM2120530v1_genomic.fna/dqc_result.json
[2023-06-29 15:56:44,186] [INFO] DFAST_QC completed!
[2023-06-29 15:56:44,186] [INFO] Total running time: 0h1m3s