[2023-06-28 11:59:35,757] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:59:35,759] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:59:35,759] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb42c692-5d5f-48d0-88d3-6ac6b6feb061/dqc_reference
[2023-06-28 11:59:36,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:59:36,843] [INFO] Task started: Prodigal
[2023-06-28 11:59:36,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg181a50ab-d244-4ac7-bb62-f2432c516426/GCA_020073375.1_ASM2007337v1_genomic.fna.gz | prodigal -d GCA_020073375.1_ASM2007337v1_genomic.fna/cds.fna -a GCA_020073375.1_ASM2007337v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:59:50,540] [INFO] Task succeeded: Prodigal
[2023-06-28 11:59:50,541] [INFO] Task started: HMMsearch
[2023-06-28 11:59:50,541] [INFO] Running command: hmmsearch --tblout GCA_020073375.1_ASM2007337v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb42c692-5d5f-48d0-88d3-6ac6b6feb061/dqc_reference/reference_markers.hmm GCA_020073375.1_ASM2007337v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:59:50,771] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:59:50,772] [INFO] Found 6/6 markers.
[2023-06-28 11:59:50,808] [INFO] Query marker FASTA was written to GCA_020073375.1_ASM2007337v1_genomic.fna/markers.fasta
[2023-06-28 11:59:50,809] [INFO] Task started: Blastn
[2023-06-28 11:59:50,809] [INFO] Running command: blastn -query GCA_020073375.1_ASM2007337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb42c692-5d5f-48d0-88d3-6ac6b6feb061/dqc_reference/reference_markers.fasta -out GCA_020073375.1_ASM2007337v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:59:51,393] [INFO] Task succeeded: Blastn
[2023-06-28 11:59:51,396] [INFO] Selected 25 target genomes.
[2023-06-28 11:59:51,396] [INFO] Target genome list was writen to GCA_020073375.1_ASM2007337v1_genomic.fna/target_genomes.txt
[2023-06-28 11:59:51,414] [INFO] Task started: fastANI
[2023-06-28 11:59:51,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg181a50ab-d244-4ac7-bb62-f2432c516426/GCA_020073375.1_ASM2007337v1_genomic.fna.gz --refList GCA_020073375.1_ASM2007337v1_genomic.fna/target_genomes.txt --output GCA_020073375.1_ASM2007337v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:00:10,124] [INFO] Task succeeded: fastANI
[2023-06-28 12:00:10,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb42c692-5d5f-48d0-88d3-6ac6b6feb061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:00:10,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb42c692-5d5f-48d0-88d3-6ac6b6feb061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:00:10,131] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:00:10,131] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:00:10,131] [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
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.9576	62	1677	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	74.8609	59	1677	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	74.8376	51	1677	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.7982	54	1677	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:00:10,133] [INFO] DFAST Taxonomy check result was written to GCA_020073375.1_ASM2007337v1_genomic.fna/tc_result.tsv
[2023-06-28 12:00:10,133] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:00:10,133] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:00:10,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb42c692-5d5f-48d0-88d3-6ac6b6feb061/dqc_reference/checkm_data
[2023-06-28 12:00:10,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:00:10,185] [INFO] Task started: CheckM
[2023-06-28 12:00:10,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020073375.1_ASM2007337v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020073375.1_ASM2007337v1_genomic.fna/checkm_input GCA_020073375.1_ASM2007337v1_genomic.fna/checkm_result
[2023-06-28 12:00:49,735] [INFO] Task succeeded: CheckM
[2023-06-28 12:00:49,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:00:49,752] [INFO] ===== Completeness check finished =====
[2023-06-28 12:00:49,752] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:00:49,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020073375.1_ASM2007337v1_genomic.fna/markers.fasta)
[2023-06-28 12:00:49,754] [INFO] Task started: Blastn
[2023-06-28 12:00:49,754] [INFO] Running command: blastn -query GCA_020073375.1_ASM2007337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb42c692-5d5f-48d0-88d3-6ac6b6feb061/dqc_reference/reference_markers_gtdb.fasta -out GCA_020073375.1_ASM2007337v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:00:50,714] [INFO] Task succeeded: Blastn
[2023-06-28 12:00:50,724] [INFO] Selected 14 target genomes.
[2023-06-28 12:00:50,724] [INFO] Target genome list was writen to GCA_020073375.1_ASM2007337v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:00:50,734] [INFO] Task started: fastANI
[2023-06-28 12:00:50,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg181a50ab-d244-4ac7-bb62-f2432c516426/GCA_020073375.1_ASM2007337v1_genomic.fna.gz --refList GCA_020073375.1_ASM2007337v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020073375.1_ASM2007337v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:01:01,881] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:01,890] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:01:01,890] [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_003165465.1	s__Palsa-360 sp003165465	78.4901	540	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Palsa-360	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161495.1	s__Palsa-360 sp003161495	77.9576	379	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Palsa-360	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016201285.1	s__JACQDE01 sp016201285	76.9108	137	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__JACQDE01	95.0	99.95	99.95	0.96	0.96	2	-
GCA_010365215.1	s__JAAFGT01 sp010365215	76.8789	123	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__JAAFGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016201215.1	s__QHYU01 sp016201215	76.8479	167	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__QHYU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003224235.1	s__QHYU01 sp003224235	76.6814	148	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__QHYU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289715.1	s__Palsa-295 sp013289715	76.6061	131	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Palsa-295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140295.1	s__Palsa-189 sp003140295	76.5072	108	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Palsa-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289695.1	s__Palsa-295 sp013289695	76.4569	130	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Palsa-295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003154775.1	s__Acidoferrum sp003154775	76.45	123	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	99.95	99.89	0.97	0.96	6	-
GCA_002478115.1	s__Acidoferrum typicum	76.3841	117	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289835.1	s__Acidoferrum sp013289835	76.3177	107	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239815.1	s__Acidoferrum sp019239815	75.5813	65	1677	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__Acidoferrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:01:01,891] [INFO] GTDB search result was written to GCA_020073375.1_ASM2007337v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:01:01,892] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:01:01,894] [INFO] DFAST_QC result json was written to GCA_020073375.1_ASM2007337v1_genomic.fna/dqc_result.json
[2023-06-28 12:01:01,895] [INFO] DFAST_QC completed!
[2023-06-28 12:01:01,895] [INFO] Total running time: 0h1m26s