[2023-06-08 09:17:21,388] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:17:21,391] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:17:21,391] [INFO] DQC Reference Directory: /var/lib/cwl/stge0cff5df-7d7e-4495-b33c-e81db74fa56a/dqc_reference
[2023-06-08 09:17:22,665] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:17:22,666] [INFO] Task started: Prodigal
[2023-06-08 09:17:22,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg963e3301-ea07-4046-8bf4-6b842a25ef44/GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:17:26,064] [INFO] Task succeeded: Prodigal
[2023-06-08 09:17:26,064] [INFO] Task started: HMMsearch
[2023-06-08 09:17:26,064] [INFO] Running command: hmmsearch --tblout GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0cff5df-7d7e-4495-b33c-e81db74fa56a/dqc_reference/reference_markers.hmm GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:17:26,307] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:17:26,308] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg963e3301-ea07-4046-8bf4-6b842a25ef44/GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 09:17:26,326] [INFO] Query marker FASTA was written to GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:17:26,326] [INFO] Task started: Blastn
[2023-06-08 09:17:26,327] [INFO] Running command: blastn -query GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge0cff5df-7d7e-4495-b33c-e81db74fa56a/dqc_reference/reference_markers.fasta -out GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:17:26,969] [INFO] Task succeeded: Blastn
[2023-06-08 09:17:26,974] [INFO] Selected 20 target genomes.
[2023-06-08 09:17:26,974] [INFO] Target genome list was writen to GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:17:26,978] [INFO] Task started: fastANI
[2023-06-08 09:17:26,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg963e3301-ea07-4046-8bf4-6b842a25ef44/GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:17:37,829] [INFO] Task succeeded: fastANI
[2023-06-08 09:17:37,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0cff5df-7d7e-4495-b33c-e81db74fa56a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:17:37,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0cff5df-7d7e-4495-b33c-e81db74fa56a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:17:37,832] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:17:37,832] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:17:37,833] [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
--------------------------------------------------------------------------------
[2023-06-08 09:17:37,835] [INFO] DFAST Taxonomy check result was written to GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:17:37,836] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:17:37,836] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:17:37,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0cff5df-7d7e-4495-b33c-e81db74fa56a/dqc_reference/checkm_data
[2023-06-08 09:17:37,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:17:37,865] [INFO] Task started: CheckM
[2023-06-08 09:17:37,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:17:55,573] [INFO] Task succeeded: CheckM
[2023-06-08 09:17:55,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.56%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 09:17:55,595] [INFO] ===== Completeness check finished =====
[2023-06-08 09:17:55,595] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:17:55,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:17:55,596] [INFO] Task started: Blastn
[2023-06-08 09:17:55,596] [INFO] Running command: blastn -query GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge0cff5df-7d7e-4495-b33c-e81db74fa56a/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:17:56,553] [INFO] Task succeeded: Blastn
[2023-06-08 09:17:56,557] [INFO] Selected 7 target genomes.
[2023-06-08 09:17:56,558] [INFO] Target genome list was writen to GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:17:56,559] [INFO] Task started: fastANI
[2023-06-08 09:17:56,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg963e3301-ea07-4046-8bf4-6b842a25ef44/GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:17:59,213] [INFO] Task succeeded: fastANI
[2023-06-08 09:17:59,219] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:17:59,220] [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_900770255.1	s__CAG-177 sp900770255	97.522	363	427	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	conclusive
GCA_003514385.1	s__CAG-177 sp003514385	81.3755	299	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	96.45	96.03	0.91	0.84	20	-
GCA_002451755.1	s__CAG-177 sp002451755	81.182	270	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	95.98	95.98	0.88	0.88	2	-
GCA_002438685.1	s__CAG-177 sp002438685	81.062	278	427	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	-
GCA_003538135.1	s__CAG-177 sp003538135	80.8567	296	427	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	98.02	97.73	0.92	0.88	9	-
--------------------------------------------------------------------------------
[2023-06-08 09:17:59,231] [INFO] GTDB search result was written to GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:17:59,232] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:17:59,235] [INFO] DFAST_QC result json was written to GCA_945831705.1_SRR5976184_bin.9_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:17:59,235] [INFO] DFAST_QC completed!
[2023-06-08 09:17:59,236] [INFO] Total running time: 0h0m38s