[2023-06-18 21:38:40,752] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:38:40,754] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:38:40,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg078d1d40-b51e-4d5f-8516-755f046c8543/dqc_reference
[2023-06-18 21:38:42,725] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:38:42,727] [INFO] Task started: Prodigal
[2023-06-18 21:38:42,727] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dc765fb-dc18-4e6a-9783-b6e06228cf2f/GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:38:48,450] [INFO] Task succeeded: Prodigal
[2023-06-18 21:38:48,451] [INFO] Task started: HMMsearch
[2023-06-18 21:38:48,451] [INFO] Running command: hmmsearch --tblout GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg078d1d40-b51e-4d5f-8516-755f046c8543/dqc_reference/reference_markers.hmm GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:38:48,643] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:38:48,646] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0dc765fb-dc18-4e6a-9783-b6e06228cf2f/GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-18 21:38:48,668] [INFO] Query marker FASTA was written to GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 21:38:48,669] [INFO] Task started: Blastn
[2023-06-18 21:38:48,669] [INFO] Running command: blastn -query GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg078d1d40-b51e-4d5f-8516-755f046c8543/dqc_reference/reference_markers.fasta -out GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:38:49,146] [INFO] Task succeeded: Blastn
[2023-06-18 21:38:49,149] [INFO] Selected 9 target genomes.
[2023-06-18 21:38:49,150] [INFO] Target genome list was writen to GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 21:38:49,170] [INFO] Task started: fastANI
[2023-06-18 21:38:49,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc765fb-dc18-4e6a-9783-b6e06228cf2f/GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:38:52,668] [INFO] Task succeeded: fastANI
[2023-06-18 21:38:52,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg078d1d40-b51e-4d5f-8516-755f046c8543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:38:52,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg078d1d40-b51e-4d5f-8516-755f046c8543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:38:52,671] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:38:52,672] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 21:38:52,672] [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
--------------------------------------------------------------------------------
[2023-06-18 21:38:52,674] [INFO] DFAST Taxonomy check result was written to GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 21:38:52,675] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:38:52,675] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:38:52,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg078d1d40-b51e-4d5f-8516-755f046c8543/dqc_reference/checkm_data
[2023-06-18 21:38:52,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:38:52,698] [INFO] Task started: CheckM
[2023-06-18 21:38:52,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 21:39:14,691] [INFO] Task succeeded: CheckM
[2023-06-18 21:39:14,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:39:14,720] [INFO] ===== Completeness check finished =====
[2023-06-18 21:39:14,721] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:39:14,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 21:39:14,722] [INFO] Task started: Blastn
[2023-06-18 21:39:14,722] [INFO] Running command: blastn -query GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg078d1d40-b51e-4d5f-8516-755f046c8543/dqc_reference/reference_markers_gtdb.fasta -out GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:39:15,165] [INFO] Task succeeded: Blastn
[2023-06-18 21:39:15,172] [INFO] Selected 17 target genomes.
[2023-06-18 21:39:15,172] [INFO] Target genome list was writen to GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:39:15,180] [INFO] Task started: fastANI
[2023-06-18 21:39:15,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc765fb-dc18-4e6a-9783-b6e06228cf2f/GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:39:22,022] [INFO] Task succeeded: fastANI
[2023-06-18 21:39:22,029] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:39:22,030] [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_000163695.1	s__F0058 sp000163695	96.9767	289	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__F0058	95.0	97.13	97.13	0.91	0.91	2	conclusive
GCA_905372135.1	s__F0058 sp905372135	89.7957	171	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__F0058	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372605.1	s__F0058 sp905372605	79.1085	71	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__F0058	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000768855.1	s__F0058 sp000768855	78.8658	83	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__F0058	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 21:39:22,034] [INFO] GTDB search result was written to GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 21:39:22,035] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:39:22,037] [INFO] DFAST_QC result json was written to GCA_915067005.1_SRR1044032_bin.1_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 21:39:22,037] [INFO] DFAST_QC completed!
[2023-06-18 21:39:22,038] [INFO] Total running time: 0h0m41s