[2024-01-25 19:06:20,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:20,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:20,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b766a32-ae97-4cf7-a889-8edbc4b98d04/dqc_reference
[2024-01-25 19:06:21,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:21,719] [INFO] Task started: Prodigal
[2024-01-25 19:06:21,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg945361d9-177a-4f9b-9f51-7a4d270ce20f/GCF_009910325.1_ASM991032v1_genomic.fna.gz | prodigal -d GCF_009910325.1_ASM991032v1_genomic.fna/cds.fna -a GCF_009910325.1_ASM991032v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:28,076] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:28,076] [INFO] Task started: HMMsearch
[2024-01-25 19:06:28,076] [INFO] Running command: hmmsearch --tblout GCF_009910325.1_ASM991032v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b766a32-ae97-4cf7-a889-8edbc4b98d04/dqc_reference/reference_markers.hmm GCF_009910325.1_ASM991032v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:28,301] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:28,302] [INFO] Found 6/6 markers.
[2024-01-25 19:06:28,328] [INFO] Query marker FASTA was written to GCF_009910325.1_ASM991032v1_genomic.fna/markers.fasta
[2024-01-25 19:06:28,328] [INFO] Task started: Blastn
[2024-01-25 19:06:28,328] [INFO] Running command: blastn -query GCF_009910325.1_ASM991032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b766a32-ae97-4cf7-a889-8edbc4b98d04/dqc_reference/reference_markers.fasta -out GCF_009910325.1_ASM991032v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:28,912] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:28,917] [INFO] Selected 17 target genomes.
[2024-01-25 19:06:28,918] [INFO] Target genome list was writen to GCF_009910325.1_ASM991032v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:28,928] [INFO] Task started: fastANI
[2024-01-25 19:06:28,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg945361d9-177a-4f9b-9f51-7a4d270ce20f/GCF_009910325.1_ASM991032v1_genomic.fna.gz --refList GCF_009910325.1_ASM991032v1_genomic.fna/target_genomes.txt --output GCF_009910325.1_ASM991032v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:39,297] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:39,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b766a32-ae97-4cf7-a889-8edbc4b98d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:39,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b766a32-ae97-4cf7-a889-8edbc4b98d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:39,300] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:06:39,300] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-25 19:06:39,300] [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
--------------------------------------------------------------------------------
[2024-01-25 19:06:39,301] [INFO] DFAST Taxonomy check result was written to GCF_009910325.1_ASM991032v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:39,302] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:39,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:39,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b766a32-ae97-4cf7-a889-8edbc4b98d04/dqc_reference/checkm_data
[2024-01-25 19:06:39,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:39,337] [INFO] Task started: CheckM
[2024-01-25 19:06:39,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009910325.1_ASM991032v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009910325.1_ASM991032v1_genomic.fna/checkm_input GCF_009910325.1_ASM991032v1_genomic.fna/checkm_result
[2024-01-25 19:07:02,694] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:02,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:02,714] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:02,714] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:02,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009910325.1_ASM991032v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:02,715] [INFO] Task started: Blastn
[2024-01-25 19:07:02,715] [INFO] Running command: blastn -query GCF_009910325.1_ASM991032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b766a32-ae97-4cf7-a889-8edbc4b98d04/dqc_reference/reference_markers_gtdb.fasta -out GCF_009910325.1_ASM991032v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:03,746] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:03,750] [INFO] Selected 14 target genomes.
[2024-01-25 19:07:03,750] [INFO] Target genome list was writen to GCF_009910325.1_ASM991032v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:03,769] [INFO] Task started: fastANI
[2024-01-25 19:07:03,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg945361d9-177a-4f9b-9f51-7a4d270ce20f/GCF_009910325.1_ASM991032v1_genomic.fna.gz --refList GCF_009910325.1_ASM991032v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009910325.1_ASM991032v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:11,732] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:11,737] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:11,737] [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_009910325.1	s__Isachenkonia alkalipeptolytica	100.0	1019	1022	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__T1SED10-28;g__Isachenkonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003553525.1	s__Isachenkonia sp003553525	81.5389	512	1022	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__T1SED10-28;g__Isachenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118655.1	s__Isachenkonia sp007118655	80.6873	292	1022	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__T1SED10-28;g__Isachenkonia	95.0	99.38	99.38	0.73	0.73	2	-
GCA_007134725.1	s__Isachenkonia sp007134725	79.951	334	1022	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__T1SED10-28;g__Isachenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120165.1	s__Isachenkonia sp007120165	79.2619	330	1022	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__T1SED10-28;g__Isachenkonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:11,739] [INFO] GTDB search result was written to GCF_009910325.1_ASM991032v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:11,739] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:11,741] [INFO] DFAST_QC result json was written to GCF_009910325.1_ASM991032v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:11,741] [INFO] DFAST_QC completed!
[2024-01-25 19:07:11,741] [INFO] Total running time: 0h0m51s