[2023-06-13 08:07:58,619] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:58,622] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:58,622] [INFO] DQC Reference Directory: /var/lib/cwl/stgc175058a-5a61-42ce-8b08-93d0f29be719/dqc_reference
[2023-06-13 08:07:59,946] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:59,947] [INFO] Task started: Prodigal
[2023-06-13 08:07:59,947] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f584791-be05-48f0-ba27-6687ac015b3f/GCA_022706045.1_ASM2270604v1_genomic.fna.gz | prodigal -d GCA_022706045.1_ASM2270604v1_genomic.fna/cds.fna -a GCA_022706045.1_ASM2270604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:08:22,014] [INFO] Task succeeded: Prodigal
[2023-06-13 08:08:22,015] [INFO] Task started: HMMsearch
[2023-06-13 08:08:22,015] [INFO] Running command: hmmsearch --tblout GCA_022706045.1_ASM2270604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc175058a-5a61-42ce-8b08-93d0f29be719/dqc_reference/reference_markers.hmm GCA_022706045.1_ASM2270604v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:08:22,380] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:08:22,382] [INFO] Found 6/6 markers.
[2023-06-13 08:08:22,436] [INFO] Query marker FASTA was written to GCA_022706045.1_ASM2270604v1_genomic.fna/markers.fasta
[2023-06-13 08:08:22,436] [INFO] Task started: Blastn
[2023-06-13 08:08:22,437] [INFO] Running command: blastn -query GCA_022706045.1_ASM2270604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc175058a-5a61-42ce-8b08-93d0f29be719/dqc_reference/reference_markers.fasta -out GCA_022706045.1_ASM2270604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:23,025] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:23,029] [INFO] Selected 25 target genomes.
[2023-06-13 08:08:23,030] [INFO] Target genome list was writen to GCA_022706045.1_ASM2270604v1_genomic.fna/target_genomes.txt
[2023-06-13 08:08:23,034] [INFO] Task started: fastANI
[2023-06-13 08:08:23,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f584791-be05-48f0-ba27-6687ac015b3f/GCA_022706045.1_ASM2270604v1_genomic.fna.gz --refList GCA_022706045.1_ASM2270604v1_genomic.fna/target_genomes.txt --output GCA_022706045.1_ASM2270604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:08:44,302] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:44,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc175058a-5a61-42ce-8b08-93d0f29be719/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:08:44,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc175058a-5a61-42ce-8b08-93d0f29be719/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:08:44,309] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:08:44,310] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:08:44,310] [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
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.5453	54	2062	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:08:44,312] [INFO] DFAST Taxonomy check result was written to GCA_022706045.1_ASM2270604v1_genomic.fna/tc_result.tsv
[2023-06-13 08:08:44,313] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:08:44,313] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:08:44,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc175058a-5a61-42ce-8b08-93d0f29be719/dqc_reference/checkm_data
[2023-06-13 08:08:44,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:08:44,381] [INFO] Task started: CheckM
[2023-06-13 08:08:44,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022706045.1_ASM2270604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022706045.1_ASM2270604v1_genomic.fna/checkm_input GCA_022706045.1_ASM2270604v1_genomic.fna/checkm_result
[2023-06-13 08:09:46,266] [INFO] Task succeeded: CheckM
[2023-06-13 08:09:46,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:09:46,293] [INFO] ===== Completeness check finished =====
[2023-06-13 08:09:46,294] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:09:46,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022706045.1_ASM2270604v1_genomic.fna/markers.fasta)
[2023-06-13 08:09:46,295] [INFO] Task started: Blastn
[2023-06-13 08:09:46,295] [INFO] Running command: blastn -query GCA_022706045.1_ASM2270604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc175058a-5a61-42ce-8b08-93d0f29be719/dqc_reference/reference_markers_gtdb.fasta -out GCA_022706045.1_ASM2270604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:09:47,059] [INFO] Task succeeded: Blastn
[2023-06-13 08:09:47,064] [INFO] Selected 22 target genomes.
[2023-06-13 08:09:47,064] [INFO] Target genome list was writen to GCA_022706045.1_ASM2270604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:09:47,077] [INFO] Task started: fastANI
[2023-06-13 08:09:47,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f584791-be05-48f0-ba27-6687ac015b3f/GCA_022706045.1_ASM2270604v1_genomic.fna.gz --refList GCA_022706045.1_ASM2270604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022706045.1_ASM2270604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:10:04,549] [INFO] Task succeeded: fastANI
[2023-06-13 08:10:04,554] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:10:04,555] [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_002070115.1	s__MWCO01 sp002070115	99.9645	1993	2062	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__MWCO01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016218915.1	s__JACRCQ01 sp016218915	76.0171	59	2062	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRCQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067165.1	s__Sorangium cellulosum_B	75.5764	51	2062	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:10:04,557] [INFO] GTDB search result was written to GCA_022706045.1_ASM2270604v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:10:04,557] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:10:04,560] [INFO] DFAST_QC result json was written to GCA_022706045.1_ASM2270604v1_genomic.fna/dqc_result.json
[2023-06-13 08:10:04,560] [INFO] DFAST_QC completed!
[2023-06-13 08:10:04,560] [INFO] Total running time: 0h2m6s