[2023-06-30 03:29:59,429] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:29:59,441] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:29:59,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg97daef43-ef03-4f85-bd31-70c9b5b2ffca/dqc_reference
[2023-06-30 03:30:01,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:30:01,227] [INFO] Task started: Prodigal
[2023-06-30 03:30:01,228] [INFO] Running command: gunzip -c /var/lib/cwl/stg2915d9f5-5dae-4d28-a23f-6947ff365d5e/GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:30:03,569] [INFO] Task succeeded: Prodigal
[2023-06-30 03:30:03,569] [INFO] Task started: HMMsearch
[2023-06-30 03:30:03,569] [INFO] Running command: hmmsearch --tblout GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97daef43-ef03-4f85-bd31-70c9b5b2ffca/dqc_reference/reference_markers.hmm GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:30:03,749] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:30:03,751] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2915d9f5-5dae-4d28-a23f-6947ff365d5e/GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-30 03:30:03,767] [INFO] Query marker FASTA was written to GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 03:30:03,767] [INFO] Task started: Blastn
[2023-06-30 03:30:03,767] [INFO] Running command: blastn -query GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg97daef43-ef03-4f85-bd31-70c9b5b2ffca/dqc_reference/reference_markers.fasta -out GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:30:05,893] [INFO] Task succeeded: Blastn
[2023-06-30 03:30:05,897] [INFO] Selected 21 target genomes.
[2023-06-30 03:30:05,898] [INFO] Target genome list was writen to GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 03:30:05,899] [INFO] Task started: fastANI
[2023-06-30 03:30:05,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg2915d9f5-5dae-4d28-a23f-6947ff365d5e/GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:30:15,487] [INFO] Task succeeded: fastANI
[2023-06-30 03:30:15,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97daef43-ef03-4f85-bd31-70c9b5b2ffca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:30:15,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97daef43-ef03-4f85-bd31-70c9b5b2ffca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:30:15,489] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:30:15,489] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 03:30:15,489] [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
--------------------------------------------------------------------------------
[2023-06-30 03:30:15,491] [INFO] DFAST Taxonomy check result was written to GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 03:30:15,492] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:30:15,492] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:30:15,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97daef43-ef03-4f85-bd31-70c9b5b2ffca/dqc_reference/checkm_data
[2023-06-30 03:30:15,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:30:15,513] [INFO] Task started: CheckM
[2023-06-30 03:30:15,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 03:30:30,083] [INFO] Task succeeded: CheckM
[2023-06-30 03:30:30,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:30:30,144] [INFO] ===== Completeness check finished =====
[2023-06-30 03:30:30,144] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:30:30,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 03:30:30,145] [INFO] Task started: Blastn
[2023-06-30 03:30:30,145] [INFO] Running command: blastn -query GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg97daef43-ef03-4f85-bd31-70c9b5b2ffca/dqc_reference/reference_markers_gtdb.fasta -out GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:30:30,855] [INFO] Task succeeded: Blastn
[2023-06-30 03:30:30,859] [INFO] Selected 18 target genomes.
[2023-06-30 03:30:30,859] [INFO] Target genome list was writen to GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:30:30,864] [INFO] Task started: fastANI
[2023-06-30 03:30:30,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg2915d9f5-5dae-4d28-a23f-6947ff365d5e/GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:30:34,890] [INFO] Task succeeded: fastANI
[2023-06-30 03:30:34,895] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:30:34,895] [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_002363635.1	s__UBA3210 sp002363635	99.5457	354	495	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__UBA3210	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015059045.1	s__UBA3210 sp015059045	77.368	90	495	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	77.104	99	495	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	76.5369	56	495	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	76.2822	57	495	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	-
--------------------------------------------------------------------------------
[2023-06-30 03:30:34,897] [INFO] GTDB search result was written to GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 03:30:34,898] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:30:34,901] [INFO] DFAST_QC result json was written to GCA_946641515.1_SRR873610_bin.55_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 03:30:34,901] [INFO] DFAST_QC completed!
[2023-06-30 03:30:34,901] [INFO] Total running time: 0h0m35s