[2023-06-13 11:49:45,118] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:49:45,124] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:49:45,124] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b9f8b98-1e1a-43c0-bee3-9217fa298b15/dqc_reference
[2023-06-13 11:49:47,199] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:49:47,200] [INFO] Task started: Prodigal
[2023-06-13 11:49:47,201] [INFO] Running command: gunzip -c /var/lib/cwl/stg94d14eb0-0d25-4064-a117-192250085e6b/GCA_022716355.1_ASM2271635v1_genomic.fna.gz | prodigal -d GCA_022716355.1_ASM2271635v1_genomic.fna/cds.fna -a GCA_022716355.1_ASM2271635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:49:52,636] [INFO] Task succeeded: Prodigal
[2023-06-13 11:49:52,636] [INFO] Task started: HMMsearch
[2023-06-13 11:49:52,637] [INFO] Running command: hmmsearch --tblout GCA_022716355.1_ASM2271635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b9f8b98-1e1a-43c0-bee3-9217fa298b15/dqc_reference/reference_markers.hmm GCA_022716355.1_ASM2271635v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:49:52,883] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:49:52,884] [INFO] Found 6/6 markers.
[2023-06-13 11:49:52,911] [INFO] Query marker FASTA was written to GCA_022716355.1_ASM2271635v1_genomic.fna/markers.fasta
[2023-06-13 11:49:52,912] [INFO] Task started: Blastn
[2023-06-13 11:49:52,912] [INFO] Running command: blastn -query GCA_022716355.1_ASM2271635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b9f8b98-1e1a-43c0-bee3-9217fa298b15/dqc_reference/reference_markers.fasta -out GCA_022716355.1_ASM2271635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:49:53,548] [INFO] Task succeeded: Blastn
[2023-06-13 11:49:53,552] [INFO] Selected 17 target genomes.
[2023-06-13 11:49:53,553] [INFO] Target genome list was writen to GCA_022716355.1_ASM2271635v1_genomic.fna/target_genomes.txt
[2023-06-13 11:49:53,557] [INFO] Task started: fastANI
[2023-06-13 11:49:53,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg94d14eb0-0d25-4064-a117-192250085e6b/GCA_022716355.1_ASM2271635v1_genomic.fna.gz --refList GCA_022716355.1_ASM2271635v1_genomic.fna/target_genomes.txt --output GCA_022716355.1_ASM2271635v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:50:02,008] [INFO] Task succeeded: fastANI
[2023-06-13 11:50:02,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b9f8b98-1e1a-43c0-bee3-9217fa298b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:50:02,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b9f8b98-1e1a-43c0-bee3-9217fa298b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:50:02,011] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:50:02,011] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 11:50:02,012] [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
--------------------------------------------------------------------------------
[2023-06-13 11:50:02,014] [INFO] DFAST Taxonomy check result was written to GCA_022716355.1_ASM2271635v1_genomic.fna/tc_result.tsv
[2023-06-13 11:50:02,015] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:50:02,016] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:50:02,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b9f8b98-1e1a-43c0-bee3-9217fa298b15/dqc_reference/checkm_data
[2023-06-13 11:50:02,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:50:02,049] [INFO] Task started: CheckM
[2023-06-13 11:50:02,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022716355.1_ASM2271635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022716355.1_ASM2271635v1_genomic.fna/checkm_input GCA_022716355.1_ASM2271635v1_genomic.fna/checkm_result
[2023-06-13 11:50:24,395] [INFO] Task succeeded: CheckM
[2023-06-13 11:50:24,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:50:24,425] [INFO] ===== Completeness check finished =====
[2023-06-13 11:50:24,425] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:50:24,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022716355.1_ASM2271635v1_genomic.fna/markers.fasta)
[2023-06-13 11:50:24,426] [INFO] Task started: Blastn
[2023-06-13 11:50:24,426] [INFO] Running command: blastn -query GCA_022716355.1_ASM2271635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b9f8b98-1e1a-43c0-bee3-9217fa298b15/dqc_reference/reference_markers_gtdb.fasta -out GCA_022716355.1_ASM2271635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:50:25,440] [INFO] Task succeeded: Blastn
[2023-06-13 11:50:25,445] [INFO] Selected 28 target genomes.
[2023-06-13 11:50:25,446] [INFO] Target genome list was writen to GCA_022716355.1_ASM2271635v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:50:25,498] [INFO] Task started: fastANI
[2023-06-13 11:50:25,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg94d14eb0-0d25-4064-a117-192250085e6b/GCA_022716355.1_ASM2271635v1_genomic.fna.gz --refList GCA_022716355.1_ASM2271635v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022716355.1_ASM2271635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:50:36,561] [INFO] Task succeeded: fastANI
[2023-06-13 11:50:36,569] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:50:36,570] [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_000436335.1	s__CAG-217 sp000436335	97.1193	496	549	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-217	95.0	97.66	96.86	0.92	0.85	21	conclusive
GCA_900547275.1	s__CAG-217 sp900547275	76.7928	80	549	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-217	95.0	99.93	99.93	0.91	0.91	2	-
GCA_900546735.1	s__Scybalenecus merdavium	76.7013	67	549	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Scybalenecus	95.0	97.85	97.41	0.89	0.76	6	-
--------------------------------------------------------------------------------
[2023-06-13 11:50:36,572] [INFO] GTDB search result was written to GCA_022716355.1_ASM2271635v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:50:36,572] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:50:36,575] [INFO] DFAST_QC result json was written to GCA_022716355.1_ASM2271635v1_genomic.fna/dqc_result.json
[2023-06-13 11:50:36,575] [INFO] DFAST_QC completed!
[2023-06-13 11:50:36,575] [INFO] Total running time: 0h0m51s