[2023-06-29 22:05:20,126] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:05:20,128] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:05:20,128] [INFO] DQC Reference Directory: /var/lib/cwl/stgc36b2a2c-e367-4295-841d-de3e78ff84c2/dqc_reference
[2023-06-29 22:05:21,314] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:05:21,315] [INFO] Task started: Prodigal
[2023-06-29 22:05:21,315] [INFO] Running command: gunzip -c /var/lib/cwl/stg01c7fad7-006d-46f2-8120-0f828afbfb5e/GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:05:24,802] [INFO] Task succeeded: Prodigal
[2023-06-29 22:05:24,802] [INFO] Task started: HMMsearch
[2023-06-29 22:05:24,802] [INFO] Running command: hmmsearch --tblout GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc36b2a2c-e367-4295-841d-de3e78ff84c2/dqc_reference/reference_markers.hmm GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:05:24,985] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:05:24,986] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg01c7fad7-006d-46f2-8120-0f828afbfb5e/GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-29 22:05:25,008] [INFO] Query marker FASTA was written to GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 22:05:25,008] [INFO] Task started: Blastn
[2023-06-29 22:05:25,009] [INFO] Running command: blastn -query GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc36b2a2c-e367-4295-841d-de3e78ff84c2/dqc_reference/reference_markers.fasta -out GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:05:25,565] [INFO] Task succeeded: Blastn
[2023-06-29 22:05:25,569] [INFO] Selected 12 target genomes.
[2023-06-29 22:05:25,569] [INFO] Target genome list was writen to GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 22:05:25,571] [INFO] Task started: fastANI
[2023-06-29 22:05:25,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c7fad7-006d-46f2-8120-0f828afbfb5e/GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:05:32,293] [INFO] Task succeeded: fastANI
[2023-06-29 22:05:32,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc36b2a2c-e367-4295-841d-de3e78ff84c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:05:32,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc36b2a2c-e367-4295-841d-de3e78ff84c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:05:32,295] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:05:32,295] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:05:32,295] [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
--------------------------------------------------------------------------------
[2023-06-29 22:05:32,297] [INFO] DFAST Taxonomy check result was written to GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 22:05:32,297] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:05:32,297] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:05:32,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc36b2a2c-e367-4295-841d-de3e78ff84c2/dqc_reference/checkm_data
[2023-06-29 22:05:32,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:05:32,320] [INFO] Task started: CheckM
[2023-06-29 22:05:32,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 22:05:49,546] [INFO] Task succeeded: CheckM
[2023-06-29 22:05:49,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 22:05:49,573] [INFO] ===== Completeness check finished =====
[2023-06-29 22:05:49,574] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:05:49,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 22:05:49,574] [INFO] Task started: Blastn
[2023-06-29 22:05:49,574] [INFO] Running command: blastn -query GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc36b2a2c-e367-4295-841d-de3e78ff84c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:05:50,540] [INFO] Task succeeded: Blastn
[2023-06-29 22:05:50,544] [INFO] Selected 21 target genomes.
[2023-06-29 22:05:50,544] [INFO] Target genome list was writen to GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:05:50,596] [INFO] Task started: fastANI
[2023-06-29 22:05:50,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c7fad7-006d-46f2-8120-0f828afbfb5e/GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:05:58,215] [INFO] Task succeeded: fastANI
[2023-06-29 22:05:58,224] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:05:58,224] [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_002440045.1	s__DTU089 sp002440045	96.2312	412	519	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__DTU089	95.0	96.25	96.25	0.75	0.75	3	conclusive
GCA_017621885.1	s__DTU089 sp017621885	77.7539	77	519	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__DTU089	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066225.1	s__DTU089 sp015066225	77.4243	106	519	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__DTU089	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626295.1	s__DTU089 sp017626295	77.2643	78	519	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__DTU089	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937865.1	s__DTU089 sp017937865	76.8884	90	519	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__DTU089	95.0	97.97	97.64	0.90	0.89	3	-
GCA_900539465.1	s__CAG-488 sp900539465	76.7848	52	519	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	99.25	98.53	0.96	0.93	3	-
GCA_015066325.1	s__DTU089 sp015066325	76.5012	60	519	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__DTU089	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015065785.1	s__DTU089 sp015065785	76.4939	59	519	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__DTU089	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297555.1	s__CAG-177 sp016297555	76.4496	50	519	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:05:58,226] [INFO] GTDB search result was written to GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 22:05:58,227] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:05:58,230] [INFO] DFAST_QC result json was written to GCA_946415085.1_SRR14812370_bin.16_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 22:05:58,230] [INFO] DFAST_QC completed!
[2023-06-29 22:05:58,230] [INFO] Total running time: 0h0m38s