[2023-06-08 14:46:11,695] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:46:11,701] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:46:11,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg9996c584-09cf-4a84-b81a-26abe0d84fb9/dqc_reference
[2023-06-08 14:46:13,747] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:46:13,749] [INFO] Task started: Prodigal
[2023-06-08 14:46:13,749] [INFO] Running command: gunzip -c /var/lib/cwl/stga90e91fa-4f32-4e65-997a-9685f402a10e/GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:46:18,528] [INFO] Task succeeded: Prodigal
[2023-06-08 14:46:18,528] [INFO] Task started: HMMsearch
[2023-06-08 14:46:18,528] [INFO] Running command: hmmsearch --tblout GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9996c584-09cf-4a84-b81a-26abe0d84fb9/dqc_reference/reference_markers.hmm GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:46:18,714] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:46:18,715] [INFO] Found 6/6 markers.
[2023-06-08 14:46:18,737] [INFO] Query marker FASTA was written to GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 14:46:18,738] [INFO] Task started: Blastn
[2023-06-08 14:46:18,738] [INFO] Running command: blastn -query GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9996c584-09cf-4a84-b81a-26abe0d84fb9/dqc_reference/reference_markers.fasta -out GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:46:19,292] [INFO] Task succeeded: Blastn
[2023-06-08 14:46:19,296] [INFO] Selected 19 target genomes.
[2023-06-08 14:46:19,296] [INFO] Target genome list was writen to GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 14:46:19,299] [INFO] Task started: fastANI
[2023-06-08 14:46:19,300] [INFO] Running command: fastANI --query /var/lib/cwl/stga90e91fa-4f32-4e65-997a-9685f402a10e/GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:46:30,682] [INFO] Task succeeded: fastANI
[2023-06-08 14:46:30,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9996c584-09cf-4a84-b81a-26abe0d84fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:46:30,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9996c584-09cf-4a84-b81a-26abe0d84fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:46:30,686] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:46:30,686] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 14:46:30,686] [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
Negativicoccus succinicivorans	strain=DSM 21255	GCA_014207605.1	620903	620903	type	True	78.7853	94	493	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:46:30,688] [INFO] DFAST Taxonomy check result was written to GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 14:46:30,689] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:46:30,689] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:46:30,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9996c584-09cf-4a84-b81a-26abe0d84fb9/dqc_reference/checkm_data
[2023-06-08 14:46:30,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:46:30,707] [INFO] Task started: CheckM
[2023-06-08 14:46:30,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 14:46:50,350] [INFO] Task succeeded: CheckM
[2023-06-08 14:46:50,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:46:50,368] [INFO] ===== Completeness check finished =====
[2023-06-08 14:46:50,369] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:46:50,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 14:46:50,369] [INFO] Task started: Blastn
[2023-06-08 14:46:50,369] [INFO] Running command: blastn -query GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9996c584-09cf-4a84-b81a-26abe0d84fb9/dqc_reference/reference_markers_gtdb.fasta -out GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:46:51,173] [INFO] Task succeeded: Blastn
[2023-06-08 14:46:51,177] [INFO] Selected 25 target genomes.
[2023-06-08 14:46:51,177] [INFO] Target genome list was writen to GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:46:51,194] [INFO] Task started: fastANI
[2023-06-08 14:46:51,195] [INFO] Running command: fastANI --query /var/lib/cwl/stga90e91fa-4f32-4e65-997a-9685f402a10e/GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:47:01,473] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:01,478] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:47:01,478] [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
GCF_902506685.1	s__Negativicoccus succinicivorans	78.6217	95	493	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Negativicoccaceae;g__Negativicoccus	95.0	97.99	97.21	0.96	0.91	6	-
GCA_900556745.1	s__Negativicoccus sp900556745	78.4063	55	493	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Negativicoccaceae;g__Negativicoccus	95.0	98.29	98.29	0.98	0.98	2	-
GCA_900155405.1	s__Negativicoccus massiliensis	77.7307	91	493	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Negativicoccaceae;g__Negativicoccus	95.0	95.18	95.18	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-08 14:47:01,480] [INFO] GTDB search result was written to GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 14:47:01,481] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:47:01,483] [INFO] DFAST_QC result json was written to GCA_945876385.1_ERR1855540_bin.6_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 14:47:01,483] [INFO] DFAST_QC completed!
[2023-06-08 14:47:01,483] [INFO] Total running time: 0h0m50s