[2023-06-13 18:13:07,838] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:13:07,840] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:13:07,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdd3ad31-2da9-46b0-bb94-f2f6054386d4/dqc_reference
[2023-06-13 18:13:08,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:13:08,976] [INFO] Task started: Prodigal
[2023-06-13 18:13:08,976] [INFO] Running command: gunzip -c /var/lib/cwl/stge676cfda-e47d-4e95-b173-af03924b97b1/GCA_022448685.1_ASM2244868v1_genomic.fna.gz | prodigal -d GCA_022448685.1_ASM2244868v1_genomic.fna/cds.fna -a GCA_022448685.1_ASM2244868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:13:13,174] [INFO] Task succeeded: Prodigal
[2023-06-13 18:13:13,174] [INFO] Task started: HMMsearch
[2023-06-13 18:13:13,174] [INFO] Running command: hmmsearch --tblout GCA_022448685.1_ASM2244868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdd3ad31-2da9-46b0-bb94-f2f6054386d4/dqc_reference/reference_markers.hmm GCA_022448685.1_ASM2244868v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:13:13,329] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:13:13,331] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge676cfda-e47d-4e95-b173-af03924b97b1/GCA_022448685.1_ASM2244868v1_genomic.fna.gz]
[2023-06-13 18:13:13,348] [INFO] Query marker FASTA was written to GCA_022448685.1_ASM2244868v1_genomic.fna/markers.fasta
[2023-06-13 18:13:13,348] [INFO] Task started: Blastn
[2023-06-13 18:13:13,349] [INFO] Running command: blastn -query GCA_022448685.1_ASM2244868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdd3ad31-2da9-46b0-bb94-f2f6054386d4/dqc_reference/reference_markers.fasta -out GCA_022448685.1_ASM2244868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:13:13,815] [INFO] Task succeeded: Blastn
[2023-06-13 18:13:13,819] [INFO] Selected 6 target genomes.
[2023-06-13 18:13:13,820] [INFO] Target genome list was writen to GCA_022448685.1_ASM2244868v1_genomic.fna/target_genomes.txt
[2023-06-13 18:13:13,821] [INFO] Task started: fastANI
[2023-06-13 18:13:13,821] [INFO] Running command: fastANI --query /var/lib/cwl/stge676cfda-e47d-4e95-b173-af03924b97b1/GCA_022448685.1_ASM2244868v1_genomic.fna.gz --refList GCA_022448685.1_ASM2244868v1_genomic.fna/target_genomes.txt --output GCA_022448685.1_ASM2244868v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:13:16,834] [INFO] Task succeeded: fastANI
[2023-06-13 18:13:16,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdd3ad31-2da9-46b0-bb94-f2f6054386d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:13:16,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdd3ad31-2da9-46b0-bb94-f2f6054386d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:13:16,836] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:13:16,836] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 18:13:16,836] [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
--------------------------------------------------------------------------------
[2023-06-13 18:13:16,838] [INFO] DFAST Taxonomy check result was written to GCA_022448685.1_ASM2244868v1_genomic.fna/tc_result.tsv
[2023-06-13 18:13:16,838] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:13:16,839] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:13:16,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdd3ad31-2da9-46b0-bb94-f2f6054386d4/dqc_reference/checkm_data
[2023-06-13 18:13:16,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:13:16,859] [INFO] Task started: CheckM
[2023-06-13 18:13:16,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448685.1_ASM2244868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448685.1_ASM2244868v1_genomic.fna/checkm_input GCA_022448685.1_ASM2244868v1_genomic.fna/checkm_result
[2023-06-13 18:13:35,353] [INFO] Task succeeded: CheckM
[2023-06-13 18:13:35,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:13:35,375] [INFO] ===== Completeness check finished =====
[2023-06-13 18:13:35,375] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:13:35,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448685.1_ASM2244868v1_genomic.fna/markers.fasta)
[2023-06-13 18:13:35,376] [INFO] Task started: Blastn
[2023-06-13 18:13:35,376] [INFO] Running command: blastn -query GCA_022448685.1_ASM2244868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdd3ad31-2da9-46b0-bb94-f2f6054386d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448685.1_ASM2244868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:13:35,857] [INFO] Task succeeded: Blastn
[2023-06-13 18:13:35,862] [INFO] Selected 9 target genomes.
[2023-06-13 18:13:35,862] [INFO] Target genome list was writen to GCA_022448685.1_ASM2244868v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:13:35,879] [INFO] Task started: fastANI
[2023-06-13 18:13:35,879] [INFO] Running command: fastANI --query /var/lib/cwl/stge676cfda-e47d-4e95-b173-af03924b97b1/GCA_022448685.1_ASM2244868v1_genomic.fna.gz --refList GCA_022448685.1_ASM2244868v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448685.1_ASM2244868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:13:38,344] [INFO] Task succeeded: fastANI
[2023-06-13 18:13:38,352] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 18:13:38,352] [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_003193925.1	s__Thalassarchaeum betae	98.0049	452	477	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.52	98.11	0.96	0.90	6	conclusive
GCA_002507125.1	s__Thalassarchaeum sp002507125	84.8873	284	477	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	79.0098	206	477	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195715.1	s__Thalassarchaeum sp004195715	78.8526	242	477	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_002498525.1	s__MGIIb-O1 sp002498525	78.1717	89	477	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	98.43	97.35	0.95	0.89	6	-
GCA_002457605.1	s__Thalassarchaeum sp002457605	78.047	158	477	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845365.1	s__MGIIb-O1 sp016845365	77.1745	53	477	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725315.1	s__MGIIb-O3 sp002725315	76.6912	51	477	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.12	98.81	0.90	0.86	5	-
--------------------------------------------------------------------------------
[2023-06-13 18:13:38,354] [INFO] GTDB search result was written to GCA_022448685.1_ASM2244868v1_genomic.fna/result_gtdb.tsv
[2023-06-13 18:13:38,355] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:13:38,359] [INFO] DFAST_QC result json was written to GCA_022448685.1_ASM2244868v1_genomic.fna/dqc_result.json
[2023-06-13 18:13:38,360] [INFO] DFAST_QC completed!
[2023-06-13 18:13:38,360] [INFO] Total running time: 0h0m31s