[2023-06-17 10:13:57,535] [INFO] DFAST_QC pipeline started.
[2023-06-17 10:13:57,545] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 10:13:57,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg4928424b-97dd-449b-9ce5-72a0ce08a962/dqc_reference
[2023-06-17 10:13:59,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 10:13:59,935] [INFO] Task started: Prodigal
[2023-06-17 10:13:59,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d083524-c665-471e-acf1-3786032b496d/GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna.gz | prodigal -d GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/cds.fna -a GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 10:14:02,281] [INFO] Task succeeded: Prodigal
[2023-06-17 10:14:02,281] [INFO] Task started: HMMsearch
[2023-06-17 10:14:02,281] [INFO] Running command: hmmsearch --tblout GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4928424b-97dd-449b-9ce5-72a0ce08a962/dqc_reference/reference_markers.hmm GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/protein.faa > /dev/null
[2023-06-17 10:14:02,497] [INFO] Task succeeded: HMMsearch
[2023-06-17 10:14:02,501] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6d083524-c665-471e-acf1-3786032b496d/GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna.gz]
[2023-06-17 10:14:02,521] [INFO] Query marker FASTA was written to GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/markers.fasta
[2023-06-17 10:14:02,521] [INFO] Task started: Blastn
[2023-06-17 10:14:02,521] [INFO] Running command: blastn -query GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stg4928424b-97dd-449b-9ce5-72a0ce08a962/dqc_reference/reference_markers.fasta -out GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:14:04,199] [INFO] Task succeeded: Blastn
[2023-06-17 10:14:04,202] [INFO] Selected 11 target genomes.
[2023-06-17 10:14:04,203] [INFO] Target genome list was writen to GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/target_genomes.txt
[2023-06-17 10:14:04,206] [INFO] Task started: fastANI
[2023-06-17 10:14:04,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d083524-c665-471e-acf1-3786032b496d/GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna.gz --refList GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/target_genomes.txt --output GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 10:14:08,627] [INFO] Task succeeded: fastANI
[2023-06-17 10:14:08,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4928424b-97dd-449b-9ce5-72a0ce08a962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 10:14:08,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4928424b-97dd-449b-9ce5-72a0ce08a962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 10:14:08,632] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 10:14:08,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 10:14:08,633] [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
Phoenicibacter congonensis	strain=Marseille-P3241	GCA_900169485.1	1944646	1944646	type	True	97.3902	131	132	95	conclusive
--------------------------------------------------------------------------------
[2023-06-17 10:14:08,635] [INFO] DFAST Taxonomy check result was written to GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/tc_result.tsv
[2023-06-17 10:14:08,635] [INFO] ===== Taxonomy check completed =====
[2023-06-17 10:14:08,636] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 10:14:08,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4928424b-97dd-449b-9ce5-72a0ce08a962/dqc_reference/checkm_data
[2023-06-17 10:14:08,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 10:14:08,655] [INFO] Task started: CheckM
[2023-06-17 10:14:08,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/checkm_input GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/checkm_result
[2023-06-17 10:14:24,043] [INFO] Task succeeded: CheckM
[2023-06-17 10:14:24,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.39%
Contamintation: 3.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-17 10:14:24,067] [INFO] ===== Completeness check finished =====
[2023-06-17 10:14:24,067] [INFO] ===== Start GTDB Search =====
[2023-06-17 10:14:24,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/markers.fasta)
[2023-06-17 10:14:24,073] [INFO] Task started: Blastn
[2023-06-17 10:14:24,074] [INFO] Running command: blastn -query GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stg4928424b-97dd-449b-9ce5-72a0ce08a962/dqc_reference/reference_markers_gtdb.fasta -out GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:14:24,784] [INFO] Task succeeded: Blastn
[2023-06-17 10:14:24,790] [INFO] Selected 16 target genomes.
[2023-06-17 10:14:24,790] [INFO] Target genome list was writen to GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 10:14:24,821] [INFO] Task started: fastANI
[2023-06-17 10:14:24,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d083524-c665-471e-acf1-3786032b496d/GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna.gz --refList GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/target_genomes_gtdb.txt --output GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 10:14:30,010] [INFO] Task succeeded: fastANI
[2023-06-17 10:14:30,015] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 10:14:30,015] [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_900169485.1	s__Phoenicibacter congonensis	97.3902	131	132	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Phoenicibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2023-06-17 10:14:30,017] [INFO] GTDB search result was written to GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/result_gtdb.tsv
[2023-06-17 10:14:30,017] [INFO] ===== GTDB Search completed =====
[2023-06-17 10:14:30,020] [INFO] DFAST_QC result json was written to GCA_905200005.1_SRR7721896-mag-bin.16_genomic.fna/dqc_result.json
[2023-06-17 10:14:30,020] [INFO] DFAST_QC completed!
[2023-06-17 10:14:30,021] [INFO] Total running time: 0h0m32s