[2023-06-30 18:02:55,372] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:02:55,376] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:02:55,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg60d4a39e-7b8f-4d73-ac49-1a4fc48aa7d4/dqc_reference
[2023-06-30 18:02:56,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:02:56,853] [INFO] Task started: Prodigal
[2023-06-30 18:02:56,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg217d470f-240b-4873-9851-4c6b0bf4aa29/GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna.gz | prodigal -d GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/cds.fna -a GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:03:01,346] [INFO] Task succeeded: Prodigal
[2023-06-30 18:03:01,347] [INFO] Task started: HMMsearch
[2023-06-30 18:03:01,347] [INFO] Running command: hmmsearch --tblout GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60d4a39e-7b8f-4d73-ac49-1a4fc48aa7d4/dqc_reference/reference_markers.hmm GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:03:01,590] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:03:01,592] [INFO] Found 6/6 markers.
[2023-06-30 18:03:01,616] [INFO] Query marker FASTA was written to GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/markers.fasta
[2023-06-30 18:03:01,616] [INFO] Task started: Blastn
[2023-06-30 18:03:01,616] [INFO] Running command: blastn -query GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg60d4a39e-7b8f-4d73-ac49-1a4fc48aa7d4/dqc_reference/reference_markers.fasta -out GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:03:03,361] [INFO] Task succeeded: Blastn
[2023-06-30 18:03:03,365] [INFO] Selected 22 target genomes.
[2023-06-30 18:03:03,366] [INFO] Target genome list was writen to GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/target_genomes.txt
[2023-06-30 18:03:03,371] [INFO] Task started: fastANI
[2023-06-30 18:03:03,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg217d470f-240b-4873-9851-4c6b0bf4aa29/GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna.gz --refList GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/target_genomes.txt --output GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:03:16,334] [INFO] Task succeeded: fastANI
[2023-06-30 18:03:16,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60d4a39e-7b8f-4d73-ac49-1a4fc48aa7d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:03:16,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60d4a39e-7b8f-4d73-ac49-1a4fc48aa7d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:03:16,339] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:03:16,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 18:03:16,339] [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
Lawsonella clevelandensis	strain=X1036	GCA_001293125.1	1528099	1528099	type	True	79.3579	249	516	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 18:03:16,342] [INFO] DFAST Taxonomy check result was written to GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/tc_result.tsv
[2023-06-30 18:03:16,343] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:03:16,343] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:03:16,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60d4a39e-7b8f-4d73-ac49-1a4fc48aa7d4/dqc_reference/checkm_data
[2023-06-30 18:03:16,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:03:16,372] [INFO] Task started: CheckM
[2023-06-30 18:03:16,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/checkm_input GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/checkm_result
[2023-06-30 18:03:36,731] [INFO] Task succeeded: CheckM
[2023-06-30 18:03:36,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:03:36,752] [INFO] ===== Completeness check finished =====
[2023-06-30 18:03:36,752] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:03:36,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/markers.fasta)
[2023-06-30 18:03:36,753] [INFO] Task started: Blastn
[2023-06-30 18:03:36,753] [INFO] Running command: blastn -query GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg60d4a39e-7b8f-4d73-ac49-1a4fc48aa7d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:03:37,699] [INFO] Task succeeded: Blastn
[2023-06-30 18:03:37,703] [INFO] Selected 21 target genomes.
[2023-06-30 18:03:37,703] [INFO] Target genome list was writen to GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:03:37,731] [INFO] Task started: fastANI
[2023-06-30 18:03:37,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg217d470f-240b-4873-9851-4c6b0bf4aa29/GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna.gz --refList GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:03:46,459] [INFO] Task succeeded: fastANI
[2023-06-30 18:03:46,469] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 18:03:46,469] [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_003241315.1	s__Lawsonella clevelandensis_A	99.9199	501	516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Lawsonella	95.0	99.91	99.91	0.96	0.96	2	conclusive
GCA_018376445.1	s__Lawsonella sp018376445	79.5165	242	516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Lawsonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293125.1	s__Lawsonella clevelandensis	79.3282	251	516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Lawsonella	95.0	99.52	99.44	0.98	0.97	4	-
GCA_012842085.1	s__Lawsonella sp012842085	78.0308	103	516	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Lawsonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:03:46,472] [INFO] GTDB search result was written to GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 18:03:46,473] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:03:46,477] [INFO] DFAST_QC result json was written to GCA_943913485.1_EnXku9qFgY_bin.1.MAG_genomic.fna/dqc_result.json
[2023-06-30 18:03:46,477] [INFO] DFAST_QC completed!
[2023-06-30 18:03:46,477] [INFO] Total running time: 0h0m51s