[2023-06-08 05:49:06,909] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:49:06,913] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:49:06,913] [INFO] DQC Reference Directory: /var/lib/cwl/stg440e176f-44bc-460c-b649-5266cfc83a27/dqc_reference
[2023-06-08 05:49:08,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:49:08,138] [INFO] Task started: Prodigal
[2023-06-08 05:49:08,138] [INFO] Running command: gunzip -c /var/lib/cwl/stgd437cfbf-6eaf-484c-83be-28f1daa1cc36/GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:49:11,455] [INFO] Task succeeded: Prodigal
[2023-06-08 05:49:11,456] [INFO] Task started: HMMsearch
[2023-06-08 05:49:11,456] [INFO] Running command: hmmsearch --tblout GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg440e176f-44bc-460c-b649-5266cfc83a27/dqc_reference/reference_markers.hmm GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:49:11,641] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:49:11,642] [INFO] Found 6/6 markers.
[2023-06-08 05:49:11,660] [INFO] Query marker FASTA was written to GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 05:49:11,661] [INFO] Task started: Blastn
[2023-06-08 05:49:11,661] [INFO] Running command: blastn -query GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg440e176f-44bc-460c-b649-5266cfc83a27/dqc_reference/reference_markers.fasta -out GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:49:12,229] [INFO] Task succeeded: Blastn
[2023-06-08 05:49:12,232] [INFO] Selected 15 target genomes.
[2023-06-08 05:49:12,232] [INFO] Target genome list was writen to GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 05:49:12,233] [INFO] Task started: fastANI
[2023-06-08 05:49:12,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgd437cfbf-6eaf-484c-83be-28f1daa1cc36/GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:49:19,874] [INFO] Task succeeded: fastANI
[2023-06-08 05:49:19,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg440e176f-44bc-460c-b649-5266cfc83a27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:49:19,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg440e176f-44bc-460c-b649-5266cfc83a27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:49:19,876] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:49:19,876] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 05:49:19,876] [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 05:49:19,878] [INFO] DFAST Taxonomy check result was written to GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 05:49:19,878] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:49:19,879] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:49:19,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg440e176f-44bc-460c-b649-5266cfc83a27/dqc_reference/checkm_data
[2023-06-08 05:49:19,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:49:19,900] [INFO] Task started: CheckM
[2023-06-08 05:49:19,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 05:49:36,847] [INFO] Task succeeded: CheckM
[2023-06-08 05:49:36,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:49:36,862] [INFO] ===== Completeness check finished =====
[2023-06-08 05:49:36,863] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:49:36,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 05:49:36,863] [INFO] Task started: Blastn
[2023-06-08 05:49:36,863] [INFO] Running command: blastn -query GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg440e176f-44bc-460c-b649-5266cfc83a27/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:49:37,617] [INFO] Task succeeded: Blastn
[2023-06-08 05:49:37,620] [INFO] Selected 20 target genomes.
[2023-06-08 05:49:37,620] [INFO] Target genome list was writen to GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:49:37,621] [INFO] Task started: fastANI
[2023-06-08 05:49:37,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgd437cfbf-6eaf-484c-83be-28f1daa1cc36/GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:49:44,668] [INFO] Task succeeded: fastANI
[2023-06-08 05:49:44,672] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 05:49:44,672] [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_900553025.1	s__S5-A14a sp900553025	78.4413	84	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__S5-A14a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000758905.1	s__S5-A14a sp000758905	78.0292	107	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__S5-A14a	95.0	96.74	96.74	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-08 05:49:44,673] [INFO] GTDB search result was written to GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 05:49:44,674] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:49:44,676] [INFO] DFAST_QC result json was written to GCA_945831845.1_SRR5240737_bin.22_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 05:49:44,676] [INFO] DFAST_QC completed!
[2023-06-08 05:49:44,676] [INFO] Total running time: 0h0m38s