[2023-06-19 12:10:35,496] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:10:35,498] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:10:35,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgd301cf0c-f2bd-43f6-b75a-024faa6b654d/dqc_reference
[2023-06-19 12:10:36,817] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:10:36,818] [INFO] Task started: Prodigal
[2023-06-19 12:10:36,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg038ccdb4-a17d-46c6-b486-e19b45878415/GCA_018623975.1_ASM1862397v1_genomic.fna.gz | prodigal -d GCA_018623975.1_ASM1862397v1_genomic.fna/cds.fna -a GCA_018623975.1_ASM1862397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:10:38,277] [INFO] Task succeeded: Prodigal
[2023-06-19 12:10:38,277] [INFO] Task started: HMMsearch
[2023-06-19 12:10:38,277] [INFO] Running command: hmmsearch --tblout GCA_018623975.1_ASM1862397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd301cf0c-f2bd-43f6-b75a-024faa6b654d/dqc_reference/reference_markers.hmm GCA_018623975.1_ASM1862397v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:10:38,490] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:10:38,491] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg038ccdb4-a17d-46c6-b486-e19b45878415/GCA_018623975.1_ASM1862397v1_genomic.fna.gz]
[2023-06-19 12:10:38,508] [INFO] Query marker FASTA was written to GCA_018623975.1_ASM1862397v1_genomic.fna/markers.fasta
[2023-06-19 12:10:38,508] [INFO] Task started: Blastn
[2023-06-19 12:10:38,508] [INFO] Running command: blastn -query GCA_018623975.1_ASM1862397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd301cf0c-f2bd-43f6-b75a-024faa6b654d/dqc_reference/reference_markers.fasta -out GCA_018623975.1_ASM1862397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:39,758] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:39,762] [INFO] Selected 0 target genomes.
[2023-06-19 12:10:39,763] [INFO] Target genome list was writen to GCA_018623975.1_ASM1862397v1_genomic.fna/target_genomes.txt
[2023-06-19 12:10:39,763] [ERROR] File is empty. [GCA_018623975.1_ASM1862397v1_genomic.fna/target_genomes.txt]
[2023-06-19 12:10:39,763] [ERROR] Task failed. No target genome found.
[2023-06-19 12:10:39,763] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:10:39,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd301cf0c-f2bd-43f6-b75a-024faa6b654d/dqc_reference/checkm_data
[2023-06-19 12:10:39,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:10:39,784] [INFO] Task started: CheckM
[2023-06-19 12:10:39,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018623975.1_ASM1862397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018623975.1_ASM1862397v1_genomic.fna/checkm_input GCA_018623975.1_ASM1862397v1_genomic.fna/checkm_result
[2023-06-19 12:10:53,795] [INFO] Task succeeded: CheckM
[2023-06-19 12:10:53,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:10:53,814] [INFO] ===== Completeness check finished =====
[2023-06-19 12:10:53,814] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:10:53,815] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018623975.1_ASM1862397v1_genomic.fna/markers.fasta)
[2023-06-19 12:10:53,815] [INFO] Task started: Blastn
[2023-06-19 12:10:53,815] [INFO] Running command: blastn -query GCA_018623975.1_ASM1862397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd301cf0c-f2bd-43f6-b75a-024faa6b654d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018623975.1_ASM1862397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:54,419] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:54,423] [INFO] Selected 5 target genomes.
[2023-06-19 12:10:54,424] [INFO] Target genome list was writen to GCA_018623975.1_ASM1862397v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:10:54,428] [INFO] Task started: fastANI
[2023-06-19 12:10:54,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg038ccdb4-a17d-46c6-b486-e19b45878415/GCA_018623975.1_ASM1862397v1_genomic.fna.gz --refList GCA_018623975.1_ASM1862397v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018623975.1_ASM1862397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:10:55,772] [INFO] Task succeeded: fastANI
[2023-06-19 12:10:55,812] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:10:55,813] [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_002686525.1	s__MGIIb-O2 sp002686525	98.2548	164	185	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.02	96.68	0.82	0.74	10	conclusive
GCA_002497245.1	s__MGIIb-O2 sp002497245	79.9025	134	185	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.50	97.50	0.90	0.90	2	-
GCA_902593945.1	s__MGIIb-O2 sp902593945	79.7067	103	185	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498985.1	s__MGIIb-O2 sp002498985	79.6105	113	185	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.30	95.20	0.78	0.62	4	-
GCA_016777225.1	s__MGIIb-O2 sp016777225	77.8477	82	185	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:10:55,815] [INFO] GTDB search result was written to GCA_018623975.1_ASM1862397v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:10:55,816] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:10:55,819] [INFO] DFAST_QC result json was written to GCA_018623975.1_ASM1862397v1_genomic.fna/dqc_result.json
[2023-06-19 12:10:55,819] [INFO] DFAST_QC completed!
[2023-06-19 12:10:55,820] [INFO] Total running time: 0h0m20s