[2023-06-28 16:15:44,260] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:15:44,262] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:15:44,262] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bf9a677-56a1-4942-9d61-f438b0dc1779/dqc_reference
[2023-06-28 16:15:45,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:15:45,464] [INFO] Task started: Prodigal
[2023-06-28 16:15:45,464] [INFO] Running command: gunzip -c /var/lib/cwl/stg488df505-8ac4-4da7-996a-7e726d427c47/GCA_012521175.1_ASM1252117v1_genomic.fna.gz | prodigal -d GCA_012521175.1_ASM1252117v1_genomic.fna/cds.fna -a GCA_012521175.1_ASM1252117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:15:49,004] [INFO] Task succeeded: Prodigal
[2023-06-28 16:15:49,005] [INFO] Task started: HMMsearch
[2023-06-28 16:15:49,005] [INFO] Running command: hmmsearch --tblout GCA_012521175.1_ASM1252117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bf9a677-56a1-4942-9d61-f438b0dc1779/dqc_reference/reference_markers.hmm GCA_012521175.1_ASM1252117v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:15:49,190] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:15:49,192] [INFO] Found 6/6 markers.
[2023-06-28 16:15:49,217] [INFO] Query marker FASTA was written to GCA_012521175.1_ASM1252117v1_genomic.fna/markers.fasta
[2023-06-28 16:15:49,217] [INFO] Task started: Blastn
[2023-06-28 16:15:49,217] [INFO] Running command: blastn -query GCA_012521175.1_ASM1252117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bf9a677-56a1-4942-9d61-f438b0dc1779/dqc_reference/reference_markers.fasta -out GCA_012521175.1_ASM1252117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:15:49,770] [INFO] Task succeeded: Blastn
[2023-06-28 16:15:49,774] [INFO] Selected 25 target genomes.
[2023-06-28 16:15:49,774] [INFO] Target genome list was writen to GCA_012521175.1_ASM1252117v1_genomic.fna/target_genomes.txt
[2023-06-28 16:15:49,811] [INFO] Task started: fastANI
[2023-06-28 16:15:49,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg488df505-8ac4-4da7-996a-7e726d427c47/GCA_012521175.1_ASM1252117v1_genomic.fna.gz --refList GCA_012521175.1_ASM1252117v1_genomic.fna/target_genomes.txt --output GCA_012521175.1_ASM1252117v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:16:01,852] [INFO] Task succeeded: fastANI
[2023-06-28 16:16:01,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bf9a677-56a1-4942-9d61-f438b0dc1779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:16:01,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bf9a677-56a1-4942-9d61-f438b0dc1779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:16:01,857] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:16:01,857] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:16:01,857] [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
Defluviitalea raffinosedens	strain=DSM 28090	GCA_016908775.1	1450156	1450156	type	True	83.0935	506	604	95	below_threshold
Defluviitalea phaphyphila	strain=Alg1	GCA_001466305.1	1473580	1473580	type	True	77.4621	189	604	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:16:01,859] [INFO] DFAST Taxonomy check result was written to GCA_012521175.1_ASM1252117v1_genomic.fna/tc_result.tsv
[2023-06-28 16:16:01,859] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:16:01,859] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:16:01,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bf9a677-56a1-4942-9d61-f438b0dc1779/dqc_reference/checkm_data
[2023-06-28 16:16:01,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:16:01,884] [INFO] Task started: CheckM
[2023-06-28 16:16:01,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012521175.1_ASM1252117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012521175.1_ASM1252117v1_genomic.fna/checkm_input GCA_012521175.1_ASM1252117v1_genomic.fna/checkm_result
[2023-06-28 16:16:19,351] [INFO] Task succeeded: CheckM
[2023-06-28 16:16:19,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:16:19,373] [INFO] ===== Completeness check finished =====
[2023-06-28 16:16:19,374] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:16:19,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012521175.1_ASM1252117v1_genomic.fna/markers.fasta)
[2023-06-28 16:16:19,374] [INFO] Task started: Blastn
[2023-06-28 16:16:19,374] [INFO] Running command: blastn -query GCA_012521175.1_ASM1252117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bf9a677-56a1-4942-9d61-f438b0dc1779/dqc_reference/reference_markers_gtdb.fasta -out GCA_012521175.1_ASM1252117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:16:20,133] [INFO] Task succeeded: Blastn
[2023-06-28 16:16:20,137] [INFO] Selected 16 target genomes.
[2023-06-28 16:16:20,137] [INFO] Target genome list was writen to GCA_012521175.1_ASM1252117v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:16:20,140] [INFO] Task started: fastANI
[2023-06-28 16:16:20,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg488df505-8ac4-4da7-996a-7e726d427c47/GCA_012521175.1_ASM1252117v1_genomic.fna.gz --refList GCA_012521175.1_ASM1252117v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012521175.1_ASM1252117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:16:28,047] [INFO] Task succeeded: fastANI
[2023-06-28 16:16:28,055] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:16:28,055] [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_012521175.1	s__Defluviitalea_A sp012521175	100.0	598	604	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012519955.1	s__Defluviitalea_A sp012519955	87.7123	468	604	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908775.1	s__Defluviitalea_A raffinosedens	83.0936	506	604	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea_A	95.0	99.48	99.46	0.95	0.94	3	-
GCF_001466305.1	s__Defluviitalea phaphyphila	77.4621	189	604	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519205.1	s__JAAYQR01 sp012519205	77.2674	121	604	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__JAAYQR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518815.1	s__JAAYML01 sp012518815	77.0462	151	604	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__JAAYML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521395.1	s__JAAYML01 sp012521395	76.8162	116	604	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__JAAYML01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:16:28,057] [INFO] GTDB search result was written to GCA_012521175.1_ASM1252117v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:16:28,058] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:16:28,061] [INFO] DFAST_QC result json was written to GCA_012521175.1_ASM1252117v1_genomic.fna/dqc_result.json
[2023-06-28 16:16:28,061] [INFO] DFAST_QC completed!
[2023-06-28 16:16:28,061] [INFO] Total running time: 0h0m44s