[2023-06-30 09:30:00,876] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:30:00,880] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:30:00,880] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4f3eaa5-7f58-49b6-a6ca-554c7595a483/dqc_reference
[2023-06-30 09:30:02,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:30:02,408] [INFO] Task started: Prodigal
[2023-06-30 09:30:02,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f838177-04ab-44ef-a3ec-5270364a4756/GCA_024694625.1_ASM2469462v1_genomic.fna.gz | prodigal -d GCA_024694625.1_ASM2469462v1_genomic.fna/cds.fna -a GCA_024694625.1_ASM2469462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:30:07,781] [INFO] Task succeeded: Prodigal
[2023-06-30 09:30:07,782] [INFO] Task started: HMMsearch
[2023-06-30 09:30:07,782] [INFO] Running command: hmmsearch --tblout GCA_024694625.1_ASM2469462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4f3eaa5-7f58-49b6-a6ca-554c7595a483/dqc_reference/reference_markers.hmm GCA_024694625.1_ASM2469462v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:30:08,021] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:30:08,023] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8f838177-04ab-44ef-a3ec-5270364a4756/GCA_024694625.1_ASM2469462v1_genomic.fna.gz]
[2023-06-30 09:30:08,048] [INFO] Query marker FASTA was written to GCA_024694625.1_ASM2469462v1_genomic.fna/markers.fasta
[2023-06-30 09:30:08,048] [INFO] Task started: Blastn
[2023-06-30 09:30:08,048] [INFO] Running command: blastn -query GCA_024694625.1_ASM2469462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f3eaa5-7f58-49b6-a6ca-554c7595a483/dqc_reference/reference_markers.fasta -out GCA_024694625.1_ASM2469462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:30:08,633] [INFO] Task succeeded: Blastn
[2023-06-30 09:30:08,638] [INFO] Selected 20 target genomes.
[2023-06-30 09:30:08,638] [INFO] Target genome list was writen to GCA_024694625.1_ASM2469462v1_genomic.fna/target_genomes.txt
[2023-06-30 09:30:08,640] [INFO] Task started: fastANI
[2023-06-30 09:30:08,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f838177-04ab-44ef-a3ec-5270364a4756/GCA_024694625.1_ASM2469462v1_genomic.fna.gz --refList GCA_024694625.1_ASM2469462v1_genomic.fna/target_genomes.txt --output GCA_024694625.1_ASM2469462v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:30:19,767] [INFO] Task succeeded: fastANI
[2023-06-30 09:30:19,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4f3eaa5-7f58-49b6-a6ca-554c7595a483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:30:19,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4f3eaa5-7f58-49b6-a6ca-554c7595a483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:30:19,774] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:30:19,774] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 09:30:19,774] [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
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	76.2329	56	716	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 09:30:19,776] [INFO] DFAST Taxonomy check result was written to GCA_024694625.1_ASM2469462v1_genomic.fna/tc_result.tsv
[2023-06-30 09:30:19,777] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:30:19,777] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:30:19,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4f3eaa5-7f58-49b6-a6ca-554c7595a483/dqc_reference/checkm_data
[2023-06-30 09:30:19,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:30:19,805] [INFO] Task started: CheckM
[2023-06-30 09:30:19,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024694625.1_ASM2469462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024694625.1_ASM2469462v1_genomic.fna/checkm_input GCA_024694625.1_ASM2469462v1_genomic.fna/checkm_result
[2023-06-30 09:30:42,801] [INFO] Task succeeded: CheckM
[2023-06-30 09:30:42,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:30:42,821] [INFO] ===== Completeness check finished =====
[2023-06-30 09:30:42,822] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:30:42,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024694625.1_ASM2469462v1_genomic.fna/markers.fasta)
[2023-06-30 09:30:42,822] [INFO] Task started: Blastn
[2023-06-30 09:30:42,822] [INFO] Running command: blastn -query GCA_024694625.1_ASM2469462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f3eaa5-7f58-49b6-a6ca-554c7595a483/dqc_reference/reference_markers_gtdb.fasta -out GCA_024694625.1_ASM2469462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:30:43,627] [INFO] Task succeeded: Blastn
[2023-06-30 09:30:43,631] [INFO] Selected 21 target genomes.
[2023-06-30 09:30:43,632] [INFO] Target genome list was writen to GCA_024694625.1_ASM2469462v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:30:43,682] [INFO] Task started: fastANI
[2023-06-30 09:30:43,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f838177-04ab-44ef-a3ec-5270364a4756/GCA_024694625.1_ASM2469462v1_genomic.fna.gz --refList GCA_024694625.1_ASM2469462v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024694625.1_ASM2469462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:30:53,597] [INFO] Task succeeded: fastANI
[2023-06-30 09:30:53,609] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 09:30:53,609] [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_905233835.1	s__XBD2001 sp905233835	78.2679	176	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__XBD2001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900116395.1	s__XBD2001 sp900116395	77.1465	77	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__XBD2001	95.0	96.26	95.68	0.91	0.86	9	-
GCA_000702525.1	s__FD2005 sp000702525	76.3001	73	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__FD2005	95.0	98.01	97.90	0.91	0.89	4	-
GCF_003478275.1	s__AM51-8 sp003478275	76.0802	56	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AM51-8	95.0	99.20	98.90	0.94	0.89	8	-
GCF_001940225.1	s__14-2 sp001940225	76.0003	53	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 09:30:53,625] [INFO] GTDB search result was written to GCA_024694625.1_ASM2469462v1_genomic.fna/result_gtdb.tsv
[2023-06-30 09:30:53,626] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:30:53,630] [INFO] DFAST_QC result json was written to GCA_024694625.1_ASM2469462v1_genomic.fna/dqc_result.json
[2023-06-30 09:30:53,630] [INFO] DFAST_QC completed!
[2023-06-30 09:30:53,630] [INFO] Total running time: 0h0m53s