[2023-06-16 23:00:04,647] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:00:04,651] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:00:04,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d60f37d-7e57-4158-90d6-f87018b5857c/dqc_reference
[2023-06-16 23:00:05,872] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:00:05,873] [INFO] Task started: Prodigal
[2023-06-16 23:00:05,873] [INFO] Running command: gunzip -c /var/lib/cwl/stg85a3451b-3ad8-46fd-bc4d-3e4f36e95669/GCA_009698715.1_ASM969871v1_genomic.fna.gz | prodigal -d GCA_009698715.1_ASM969871v1_genomic.fna/cds.fna -a GCA_009698715.1_ASM969871v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:00:08,147] [INFO] Task succeeded: Prodigal
[2023-06-16 23:00:08,148] [INFO] Task started: HMMsearch
[2023-06-16 23:00:08,148] [INFO] Running command: hmmsearch --tblout GCA_009698715.1_ASM969871v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d60f37d-7e57-4158-90d6-f87018b5857c/dqc_reference/reference_markers.hmm GCA_009698715.1_ASM969871v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:00:08,311] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:00:08,312] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg85a3451b-3ad8-46fd-bc4d-3e4f36e95669/GCA_009698715.1_ASM969871v1_genomic.fna.gz]
[2023-06-16 23:00:08,325] [INFO] Query marker FASTA was written to GCA_009698715.1_ASM969871v1_genomic.fna/markers.fasta
[2023-06-16 23:00:08,326] [INFO] Task started: Blastn
[2023-06-16 23:00:08,326] [INFO] Running command: blastn -query GCA_009698715.1_ASM969871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d60f37d-7e57-4158-90d6-f87018b5857c/dqc_reference/reference_markers.fasta -out GCA_009698715.1_ASM969871v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:00:08,975] [INFO] Task succeeded: Blastn
[2023-06-16 23:00:08,979] [INFO] Selected 6 target genomes.
[2023-06-16 23:00:08,979] [INFO] Target genome list was writen to GCA_009698715.1_ASM969871v1_genomic.fna/target_genomes.txt
[2023-06-16 23:00:08,984] [INFO] Task started: fastANI
[2023-06-16 23:00:08,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg85a3451b-3ad8-46fd-bc4d-3e4f36e95669/GCA_009698715.1_ASM969871v1_genomic.fna.gz --refList GCA_009698715.1_ASM969871v1_genomic.fna/target_genomes.txt --output GCA_009698715.1_ASM969871v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:00:12,091] [INFO] Task succeeded: fastANI
[2023-06-16 23:00:12,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d60f37d-7e57-4158-90d6-f87018b5857c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:00:12,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d60f37d-7e57-4158-90d6-f87018b5857c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:00:12,093] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:00:12,093] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 23:00:12,093] [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
--------------------------------------------------------------------------------
[2023-06-16 23:00:12,095] [INFO] DFAST Taxonomy check result was written to GCA_009698715.1_ASM969871v1_genomic.fna/tc_result.tsv
[2023-06-16 23:00:12,096] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:00:12,096] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:00:12,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d60f37d-7e57-4158-90d6-f87018b5857c/dqc_reference/checkm_data
[2023-06-16 23:00:12,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:00:12,110] [INFO] Task started: CheckM
[2023-06-16 23:00:12,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009698715.1_ASM969871v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009698715.1_ASM969871v1_genomic.fna/checkm_input GCA_009698715.1_ASM969871v1_genomic.fna/checkm_result
[2023-06-16 23:00:28,074] [INFO] Task succeeded: CheckM
[2023-06-16 23:00:28,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-16 23:00:28,094] [INFO] ===== Completeness check finished =====
[2023-06-16 23:00:28,095] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:00:28,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009698715.1_ASM969871v1_genomic.fna/markers.fasta)
[2023-06-16 23:00:28,095] [INFO] Task started: Blastn
[2023-06-16 23:00:28,095] [INFO] Running command: blastn -query GCA_009698715.1_ASM969871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d60f37d-7e57-4158-90d6-f87018b5857c/dqc_reference/reference_markers_gtdb.fasta -out GCA_009698715.1_ASM969871v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:00:28,791] [INFO] Task succeeded: Blastn
[2023-06-16 23:00:28,795] [INFO] Selected 6 target genomes.
[2023-06-16 23:00:28,796] [INFO] Target genome list was writen to GCA_009698715.1_ASM969871v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:00:28,834] [INFO] Task started: fastANI
[2023-06-16 23:00:28,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg85a3451b-3ad8-46fd-bc4d-3e4f36e95669/GCA_009698715.1_ASM969871v1_genomic.fna.gz --refList GCA_009698715.1_ASM969871v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009698715.1_ASM969871v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:00:30,725] [INFO] Task succeeded: fastANI
[2023-06-16 23:00:30,732] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 23:00:30,732] [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_009705435.1	s__Casp-actino8 sp009705435	98.8141	200	230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.36	98.35	0.80	0.80	3	conclusive
GCA_014190215.1	s__Casp-actino8 sp014190215	93.2269	198	230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694465.1	s__Casp-actino8 sp009694465	92.8382	147	230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	95.85	95.85	0.64	0.64	2	-
GCA_903872155.1	s__Casp-actino8 sp903872155	78.0903	80	230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.87	96.83	0.92	0.86	4	-
GCA_009700145.1	s__Casp-actino8 sp009700145	77.6106	62	230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	99.51	99.42	0.81	0.73	6	-
GCA_001510335.1	s__Casp-actino8 sp001510335	77.0342	53	230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 23:00:30,734] [INFO] GTDB search result was written to GCA_009698715.1_ASM969871v1_genomic.fna/result_gtdb.tsv
[2023-06-16 23:00:30,735] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:00:30,738] [INFO] DFAST_QC result json was written to GCA_009698715.1_ASM969871v1_genomic.fna/dqc_result.json
[2023-06-16 23:00:30,738] [INFO] DFAST_QC completed!
[2023-06-16 23:00:30,739] [INFO] Total running time: 0h0m26s