[2023-06-07 20:07:37,833] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:07:37,840] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:07:37,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb897ab7-f92b-49e3-bfb2-1c872b5e202f/dqc_reference
[2023-06-07 20:07:39,918] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:07:39,919] [INFO] Task started: Prodigal
[2023-06-07 20:07:39,919] [INFO] Running command: gunzip -c /var/lib/cwl/stg39858539-96c7-4720-ae6e-d67bd4fff8b1/GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:07:42,073] [INFO] Task succeeded: Prodigal
[2023-06-07 20:07:42,073] [INFO] Task started: HMMsearch
[2023-06-07 20:07:42,074] [INFO] Running command: hmmsearch --tblout GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb897ab7-f92b-49e3-bfb2-1c872b5e202f/dqc_reference/reference_markers.hmm GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:07:42,313] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:07:42,314] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg39858539-96c7-4720-ae6e-d67bd4fff8b1/GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-07 20:07:42,335] [INFO] Query marker FASTA was written to GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 20:07:42,335] [INFO] Task started: Blastn
[2023-06-07 20:07:42,336] [INFO] Running command: blastn -query GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb897ab7-f92b-49e3-bfb2-1c872b5e202f/dqc_reference/reference_markers.fasta -out GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:07:43,091] [INFO] Task succeeded: Blastn
[2023-06-07 20:07:43,095] [INFO] Selected 15 target genomes.
[2023-06-07 20:07:43,095] [INFO] Target genome list was writen to GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 20:07:43,115] [INFO] Task started: fastANI
[2023-06-07 20:07:43,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg39858539-96c7-4720-ae6e-d67bd4fff8b1/GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:07:48,621] [INFO] Task succeeded: fastANI
[2023-06-07 20:07:48,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb897ab7-f92b-49e3-bfb2-1c872b5e202f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:07:48,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb897ab7-f92b-49e3-bfb2-1c872b5e202f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:07:48,625] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:07:48,625] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 20:07:48,625] [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 20:07:48,627] [INFO] DFAST Taxonomy check result was written to GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 20:07:48,628] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:07:48,628] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:07:48,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb897ab7-f92b-49e3-bfb2-1c872b5e202f/dqc_reference/checkm_data
[2023-06-07 20:07:48,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:07:48,656] [INFO] Task started: CheckM
[2023-06-07 20:07:48,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 20:08:03,744] [INFO] Task succeeded: CheckM
[2023-06-07 20:08:03,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:08:03,763] [INFO] ===== Completeness check finished =====
[2023-06-07 20:08:03,764] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:08:03,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 20:08:03,765] [INFO] Task started: Blastn
[2023-06-07 20:08:03,765] [INFO] Running command: blastn -query GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb897ab7-f92b-49e3-bfb2-1c872b5e202f/dqc_reference/reference_markers_gtdb.fasta -out GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:08:04,511] [INFO] Task succeeded: Blastn
[2023-06-07 20:08:04,516] [INFO] Selected 15 target genomes.
[2023-06-07 20:08:04,516] [INFO] Target genome list was writen to GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:08:04,522] [INFO] Task started: fastANI
[2023-06-07 20:08:04,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg39858539-96c7-4720-ae6e-d67bd4fff8b1/GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:08:07,882] [INFO] Task succeeded: fastANI
[2023-06-07 20:08:07,890] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 20:08:07,890] [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_015059045.1	s__UBA3210 sp015059045	78.9563	157	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__UBA3210	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059095.1	s__UBA3210 sp015059095	77.4818	85	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__UBA3210	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905204225.1	s__CAG-449 sp905204225	76.8016	67	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__CAG-449	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432895.1	s__CAG-449 sp000432895	76.4278	63	461	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__CAG-449	95.0	98.56	98.56	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-07 20:08:07,892] [INFO] GTDB search result was written to GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 20:08:07,892] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:08:07,895] [INFO] DFAST_QC result json was written to GCA_945929875.1_SRR11489748_bin.60_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 20:08:07,895] [INFO] DFAST_QC completed!
[2023-06-07 20:08:07,895] [INFO] Total running time: 0h0m30s