[2023-06-08 03:14:19,631] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:14:19,633] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:14:19,633] [INFO] DQC Reference Directory: /var/lib/cwl/stga33bbe6b-2b1a-448d-ba78-ad0572d8130c/dqc_reference
[2023-06-08 03:14:21,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:14:21,137] [INFO] Task started: Prodigal
[2023-06-08 03:14:21,137] [INFO] Running command: gunzip -c /var/lib/cwl/stgf586ba22-3eb0-44fe-a705-5e8ff9d448dd/GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:14:24,325] [INFO] Task succeeded: Prodigal
[2023-06-08 03:14:24,325] [INFO] Task started: HMMsearch
[2023-06-08 03:14:24,325] [INFO] Running command: hmmsearch --tblout GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga33bbe6b-2b1a-448d-ba78-ad0572d8130c/dqc_reference/reference_markers.hmm GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:14:24,611] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:14:24,612] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf586ba22-3eb0-44fe-a705-5e8ff9d448dd/GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 03:14:24,635] [INFO] Query marker FASTA was written to GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 03:14:24,636] [INFO] Task started: Blastn
[2023-06-08 03:14:24,636] [INFO] Running command: blastn -query GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga33bbe6b-2b1a-448d-ba78-ad0572d8130c/dqc_reference/reference_markers.fasta -out GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:25,223] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:25,227] [INFO] Selected 15 target genomes.
[2023-06-08 03:14:25,228] [INFO] Target genome list was writen to GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 03:14:25,228] [INFO] Task started: fastANI
[2023-06-08 03:14:25,229] [INFO] Running command: fastANI --query /var/lib/cwl/stgf586ba22-3eb0-44fe-a705-5e8ff9d448dd/GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:14:32,970] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:32,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga33bbe6b-2b1a-448d-ba78-ad0572d8130c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:14:32,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga33bbe6b-2b1a-448d-ba78-ad0572d8130c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:14:32,973] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:14:32,973] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:14:32,973] [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 03:14:32,975] [INFO] DFAST Taxonomy check result was written to GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 03:14:32,975] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:14:32,976] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:14:32,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga33bbe6b-2b1a-448d-ba78-ad0572d8130c/dqc_reference/checkm_data
[2023-06-08 03:14:32,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:14:32,997] [INFO] Task started: CheckM
[2023-06-08 03:14:32,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 03:14:50,397] [INFO] Task succeeded: CheckM
[2023-06-08 03:14:50,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.65%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 03:14:50,420] [INFO] ===== Completeness check finished =====
[2023-06-08 03:14:50,420] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:14:50,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 03:14:50,421] [INFO] Task started: Blastn
[2023-06-08 03:14:50,421] [INFO] Running command: blastn -query GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga33bbe6b-2b1a-448d-ba78-ad0572d8130c/dqc_reference/reference_markers_gtdb.fasta -out GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:51,071] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:51,075] [INFO] Selected 13 target genomes.
[2023-06-08 03:14:51,076] [INFO] Target genome list was writen to GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:14:51,081] [INFO] Task started: fastANI
[2023-06-08 03:14:51,082] [INFO] Running command: fastANI --query /var/lib/cwl/stgf586ba22-3eb0-44fe-a705-5e8ff9d448dd/GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:14:57,664] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:57,668] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 03:14:57,668] [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_016301965.1	s__UBA11957 sp016301965	85.6523	222	341	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA11957	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:14:57,670] [INFO] GTDB search result was written to GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 03:14:57,671] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:14:57,673] [INFO] DFAST_QC result json was written to GCA_945788595.1_SRR3178346_bin.19_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 03:14:57,673] [INFO] DFAST_QC completed!
[2023-06-08 03:14:57,673] [INFO] Total running time: 0h0m38s