[2023-06-07 19:52:05,024] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:52:05,026] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:52:05,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c5e1470-0319-4e84-9e9a-f5ef3e540f29/dqc_reference
[2023-06-07 19:52:06,176] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:52:06,177] [INFO] Task started: Prodigal
[2023-06-07 19:52:06,177] [INFO] Running command: gunzip -c /var/lib/cwl/stgd23963c4-cd66-49f0-9594-6c6232ad032c/GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:52:10,221] [INFO] Task succeeded: Prodigal
[2023-06-07 19:52:10,221] [INFO] Task started: HMMsearch
[2023-06-07 19:52:10,221] [INFO] Running command: hmmsearch --tblout GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c5e1470-0319-4e84-9e9a-f5ef3e540f29/dqc_reference/reference_markers.hmm GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:52:10,439] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:52:10,441] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd23963c4-cd66-49f0-9594-6c6232ad032c/GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-07 19:52:10,463] [INFO] Query marker FASTA was written to GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 19:52:10,463] [INFO] Task started: Blastn
[2023-06-07 19:52:10,464] [INFO] Running command: blastn -query GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c5e1470-0319-4e84-9e9a-f5ef3e540f29/dqc_reference/reference_markers.fasta -out GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:52:11,062] [INFO] Task succeeded: Blastn
[2023-06-07 19:52:11,069] [INFO] Selected 19 target genomes.
[2023-06-07 19:52:11,070] [INFO] Target genome list was writen to GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 19:52:11,073] [INFO] Task started: fastANI
[2023-06-07 19:52:11,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgd23963c4-cd66-49f0-9594-6c6232ad032c/GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:52:20,923] [INFO] Task succeeded: fastANI
[2023-06-07 19:52:20,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c5e1470-0319-4e84-9e9a-f5ef3e540f29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:52:20,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c5e1470-0319-4e84-9e9a-f5ef3e540f29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:52:20,926] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:52:20,926] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 19:52:20,926] [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
--------------------------------------------------------------------------------
[2023-06-07 19:52:20,928] [INFO] DFAST Taxonomy check result was written to GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 19:52:20,929] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:52:20,929] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:52:20,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c5e1470-0319-4e84-9e9a-f5ef3e540f29/dqc_reference/checkm_data
[2023-06-07 19:52:20,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:52:20,957] [INFO] Task started: CheckM
[2023-06-07 19:52:20,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 19:52:40,071] [INFO] Task succeeded: CheckM
[2023-06-07 19:52:40,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:52:40,098] [INFO] ===== Completeness check finished =====
[2023-06-07 19:52:40,099] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:52:40,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 19:52:40,099] [INFO] Task started: Blastn
[2023-06-07 19:52:40,099] [INFO] Running command: blastn -query GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c5e1470-0319-4e84-9e9a-f5ef3e540f29/dqc_reference/reference_markers_gtdb.fasta -out GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:52:41,022] [INFO] Task succeeded: Blastn
[2023-06-07 19:52:41,027] [INFO] Selected 9 target genomes.
[2023-06-07 19:52:41,027] [INFO] Target genome list was writen to GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:52:41,033] [INFO] Task started: fastANI
[2023-06-07 19:52:41,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgd23963c4-cd66-49f0-9594-6c6232ad032c/GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:52:44,683] [INFO] Task succeeded: fastANI
[2023-06-07 19:52:44,692] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 19:52:44,692] [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_016294105.1	s__Treponema_F sp016294105	99.0957	432	441	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	97.89	97.89	0.95	0.95	2	conclusive
GCA_017549025.1	s__Treponema_F sp017549025	89.3633	415	441	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017629095.1	s__Treponema_F sp017629095	86.0592	367	441	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	97.22	97.22	0.85	0.85	3	-
GCA_017646305.1	s__Treponema_F sp017646305	85.6188	232	441	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622135.1	s__Treponema_F sp017622135	79.8908	236	441	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	96.98	95.06	0.88	0.84	7	-
GCA_017936345.1	s__Treponema_F sp017936345	79.7573	196	441	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	98.63	98.63	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-07 19:52:44,694] [INFO] GTDB search result was written to GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 19:52:44,695] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:52:44,698] [INFO] DFAST_QC result json was written to GCA_945992155.1_SRR12203180_bin.1_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 19:52:44,698] [INFO] DFAST_QC completed!
[2023-06-07 19:52:44,698] [INFO] Total running time: 0h0m40s