[2023-06-08 02:20:36,616] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:20:36,618] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:20:36,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fd4dbd2-deff-4738-9f5a-20444add2c34/dqc_reference
[2023-06-08 02:20:38,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:20:38,073] [INFO] Task started: Prodigal
[2023-06-08 02:20:38,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c726e43-65f3-4ff1-b9e5-6043eb76c212/GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:20:41,085] [INFO] Task succeeded: Prodigal
[2023-06-08 02:20:41,085] [INFO] Task started: HMMsearch
[2023-06-08 02:20:41,086] [INFO] Running command: hmmsearch --tblout GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fd4dbd2-deff-4738-9f5a-20444add2c34/dqc_reference/reference_markers.hmm GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:20:41,324] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:20:41,325] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0c726e43-65f3-4ff1-b9e5-6043eb76c212/GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 02:20:41,359] [INFO] Query marker FASTA was written to GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 02:20:41,360] [INFO] Task started: Blastn
[2023-06-08 02:20:41,360] [INFO] Running command: blastn -query GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fd4dbd2-deff-4738-9f5a-20444add2c34/dqc_reference/reference_markers.fasta -out GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:41,934] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:41,937] [INFO] Selected 20 target genomes.
[2023-06-08 02:20:41,938] [INFO] Target genome list was writen to GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 02:20:41,942] [INFO] Task started: fastANI
[2023-06-08 02:20:41,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c726e43-65f3-4ff1-b9e5-6043eb76c212/GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:20:49,612] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:49,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fd4dbd2-deff-4738-9f5a-20444add2c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:20:49,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fd4dbd2-deff-4738-9f5a-20444add2c34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:20:49,616] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:20:49,617] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 02:20:49,617] [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
--------------------------------------------------------------------------------
[2023-06-08 02:20:49,620] [INFO] DFAST Taxonomy check result was written to GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 02:20:49,621] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:20:49,621] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:20:49,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fd4dbd2-deff-4738-9f5a-20444add2c34/dqc_reference/checkm_data
[2023-06-08 02:20:49,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:20:49,648] [INFO] Task started: CheckM
[2023-06-08 02:20:49,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 02:21:07,051] [INFO] Task succeeded: CheckM
[2023-06-08 02:21:07,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:21:07,074] [INFO] ===== Completeness check finished =====
[2023-06-08 02:21:07,075] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:21:07,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 02:21:07,075] [INFO] Task started: Blastn
[2023-06-08 02:21:07,076] [INFO] Running command: blastn -query GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fd4dbd2-deff-4738-9f5a-20444add2c34/dqc_reference/reference_markers_gtdb.fasta -out GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:21:07,867] [INFO] Task succeeded: Blastn
[2023-06-08 02:21:07,871] [INFO] Selected 19 target genomes.
[2023-06-08 02:21:07,871] [INFO] Target genome list was writen to GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:21:07,881] [INFO] Task started: fastANI
[2023-06-08 02:21:07,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c726e43-65f3-4ff1-b9e5-6043eb76c212/GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:21:14,278] [INFO] Task succeeded: fastANI
[2023-06-08 02:21:14,286] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 02:21:14,287] [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_900546285.1	s__UBA636 sp900546285	95.1694	452	561	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	96.11	96.11	0.80	0.80	2	conclusive
GCA_017404205.1	s__UBA636 sp017404205	77.627	88	561	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018064825.1	s__UBA636 sp018064825	77.5299	52	561	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 02:21:14,289] [INFO] GTDB search result was written to GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 02:21:14,290] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:21:14,298] [INFO] DFAST_QC result json was written to GCA_945910625.1_SRR11489781_bin.72_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 02:21:14,298] [INFO] DFAST_QC completed!
[2023-06-08 02:21:14,298] [INFO] Total running time: 0h0m38s