[2023-06-13 15:01:47,223] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:01:47,225] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:01:47,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg1aa53941-48df-48a7-b9c4-3cf8b15ef879/dqc_reference
[2023-06-13 15:01:48,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:01:48,376] [INFO] Task started: Prodigal
[2023-06-13 15:01:48,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bd13e0a-22c8-4829-99b5-2ce3a75a58f9/GCA_022827145.1_ASM2282714v1_genomic.fna.gz | prodigal -d GCA_022827145.1_ASM2282714v1_genomic.fna/cds.fna -a GCA_022827145.1_ASM2282714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:01:59,318] [INFO] Task succeeded: Prodigal
[2023-06-13 15:01:59,318] [INFO] Task started: HMMsearch
[2023-06-13 15:01:59,318] [INFO] Running command: hmmsearch --tblout GCA_022827145.1_ASM2282714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1aa53941-48df-48a7-b9c4-3cf8b15ef879/dqc_reference/reference_markers.hmm GCA_022827145.1_ASM2282714v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:01:59,572] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:01:59,574] [INFO] Found 6/6 markers.
[2023-06-13 15:01:59,609] [INFO] Query marker FASTA was written to GCA_022827145.1_ASM2282714v1_genomic.fna/markers.fasta
[2023-06-13 15:01:59,609] [INFO] Task started: Blastn
[2023-06-13 15:01:59,610] [INFO] Running command: blastn -query GCA_022827145.1_ASM2282714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aa53941-48df-48a7-b9c4-3cf8b15ef879/dqc_reference/reference_markers.fasta -out GCA_022827145.1_ASM2282714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:02:00,195] [INFO] Task succeeded: Blastn
[2023-06-13 15:02:00,200] [INFO] Selected 24 target genomes.
[2023-06-13 15:02:00,200] [INFO] Target genome list was writen to GCA_022827145.1_ASM2282714v1_genomic.fna/target_genomes.txt
[2023-06-13 15:02:00,202] [INFO] Task started: fastANI
[2023-06-13 15:02:00,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd13e0a-22c8-4829-99b5-2ce3a75a58f9/GCA_022827145.1_ASM2282714v1_genomic.fna.gz --refList GCA_022827145.1_ASM2282714v1_genomic.fna/target_genomes.txt --output GCA_022827145.1_ASM2282714v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:02:14,092] [INFO] Task succeeded: fastANI
[2023-06-13 15:02:14,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1aa53941-48df-48a7-b9c4-3cf8b15ef879/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:02:14,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1aa53941-48df-48a7-b9c4-3cf8b15ef879/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:02:14,099] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:02:14,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:02:14,099] [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
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	74.6446	65	1283	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:02:14,101] [INFO] DFAST Taxonomy check result was written to GCA_022827145.1_ASM2282714v1_genomic.fna/tc_result.tsv
[2023-06-13 15:02:14,102] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:02:14,102] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:02:14,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1aa53941-48df-48a7-b9c4-3cf8b15ef879/dqc_reference/checkm_data
[2023-06-13 15:02:14,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:02:14,146] [INFO] Task started: CheckM
[2023-06-13 15:02:14,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022827145.1_ASM2282714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022827145.1_ASM2282714v1_genomic.fna/checkm_input GCA_022827145.1_ASM2282714v1_genomic.fna/checkm_result
[2023-06-13 15:02:49,053] [INFO] Task succeeded: CheckM
[2023-06-13 15:02:49,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:02:49,077] [INFO] ===== Completeness check finished =====
[2023-06-13 15:02:49,077] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:02:49,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022827145.1_ASM2282714v1_genomic.fna/markers.fasta)
[2023-06-13 15:02:49,078] [INFO] Task started: Blastn
[2023-06-13 15:02:49,078] [INFO] Running command: blastn -query GCA_022827145.1_ASM2282714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aa53941-48df-48a7-b9c4-3cf8b15ef879/dqc_reference/reference_markers_gtdb.fasta -out GCA_022827145.1_ASM2282714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:02:49,904] [INFO] Task succeeded: Blastn
[2023-06-13 15:02:49,912] [INFO] Selected 5 target genomes.
[2023-06-13 15:02:49,912] [INFO] Target genome list was writen to GCA_022827145.1_ASM2282714v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:02:49,913] [INFO] Task started: fastANI
[2023-06-13 15:02:49,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd13e0a-22c8-4829-99b5-2ce3a75a58f9/GCA_022827145.1_ASM2282714v1_genomic.fna.gz --refList GCA_022827145.1_ASM2282714v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022827145.1_ASM2282714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:02:54,846] [INFO] Task succeeded: fastANI
[2023-06-13 15:02:54,852] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:02:54,853] [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_009841265.1	s__JAAXHH01 sp009841265	91.296	1113	1283	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	99.97	99.96	1.00	1.00	3	-
GCA_009838645.1	s__JAAXHH01 sp009838645	91.2466	1107	1283	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	99.98	99.97	0.98	0.98	3	-
GCA_009835325.1	s__JAAXHH01 sp009835325	91.2259	1045	1283	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	99.99	99.99	1.00	1.00	2	-
GCA_009837395.1	s__JAAXHH01 sp009837395	91.0888	1096	1283	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	98.47	97.89	0.97	0.94	5	-
GCA_012270975.1	s__JAAXHH01 sp012270975	86.7986	1050	1283	d__Bacteria;p__JAAXHH01;c__JAAXHH01;o__JAAXHH01;f__JAAXHH01;g__JAAXHH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:02:54,855] [INFO] GTDB search result was written to GCA_022827145.1_ASM2282714v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:02:54,855] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:02:54,858] [INFO] DFAST_QC result json was written to GCA_022827145.1_ASM2282714v1_genomic.fna/dqc_result.json
[2023-06-13 15:02:54,858] [INFO] DFAST_QC completed!
[2023-06-13 15:02:54,858] [INFO] Total running time: 0h1m8s