[2023-06-19 00:53:11,388] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:53:11,391] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:53:11,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg5728dfb1-4ad8-4201-8b4a-8ef70c0964ca/dqc_reference
[2023-06-19 00:53:13,715] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:53:13,716] [INFO] Task started: Prodigal
[2023-06-19 00:53:13,717] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb8a07a3-9625-444a-bcad-9be260293538/GCA_018657585.1_ASM1865758v1_genomic.fna.gz | prodigal -d GCA_018657585.1_ASM1865758v1_genomic.fna/cds.fna -a GCA_018657585.1_ASM1865758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:53:18,418] [INFO] Task succeeded: Prodigal
[2023-06-19 00:53:18,418] [INFO] Task started: HMMsearch
[2023-06-19 00:53:18,418] [INFO] Running command: hmmsearch --tblout GCA_018657585.1_ASM1865758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5728dfb1-4ad8-4201-8b4a-8ef70c0964ca/dqc_reference/reference_markers.hmm GCA_018657585.1_ASM1865758v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:53:18,663] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:53:18,665] [INFO] Found 6/6 markers.
[2023-06-19 00:53:18,693] [INFO] Query marker FASTA was written to GCA_018657585.1_ASM1865758v1_genomic.fna/markers.fasta
[2023-06-19 00:53:18,693] [INFO] Task started: Blastn
[2023-06-19 00:53:18,693] [INFO] Running command: blastn -query GCA_018657585.1_ASM1865758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5728dfb1-4ad8-4201-8b4a-8ef70c0964ca/dqc_reference/reference_markers.fasta -out GCA_018657585.1_ASM1865758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:53:19,244] [INFO] Task succeeded: Blastn
[2023-06-19 00:53:19,251] [INFO] Selected 11 target genomes.
[2023-06-19 00:53:19,251] [INFO] Target genome list was writen to GCA_018657585.1_ASM1865758v1_genomic.fna/target_genomes.txt
[2023-06-19 00:53:19,254] [INFO] Task started: fastANI
[2023-06-19 00:53:19,254] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb8a07a3-9625-444a-bcad-9be260293538/GCA_018657585.1_ASM1865758v1_genomic.fna.gz --refList GCA_018657585.1_ASM1865758v1_genomic.fna/target_genomes.txt --output GCA_018657585.1_ASM1865758v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:53:23,671] [INFO] Task succeeded: fastANI
[2023-06-19 00:53:23,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5728dfb1-4ad8-4201-8b4a-8ef70c0964ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:53:23,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5728dfb1-4ad8-4201-8b4a-8ef70c0964ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:53:23,679] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:53:23,679] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 00:53:23,679] [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
--------------------------------------------------------------------------------
[2023-06-19 00:53:23,685] [INFO] DFAST Taxonomy check result was written to GCA_018657585.1_ASM1865758v1_genomic.fna/tc_result.tsv
[2023-06-19 00:53:23,686] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:53:23,686] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:53:23,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5728dfb1-4ad8-4201-8b4a-8ef70c0964ca/dqc_reference/checkm_data
[2023-06-19 00:53:23,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:53:23,718] [INFO] Task started: CheckM
[2023-06-19 00:53:23,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018657585.1_ASM1865758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018657585.1_ASM1865758v1_genomic.fna/checkm_input GCA_018657585.1_ASM1865758v1_genomic.fna/checkm_result
[2023-06-19 00:53:44,797] [INFO] Task succeeded: CheckM
[2023-06-19 00:53:44,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.81%
Contamintation: 5.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 00:53:44,842] [INFO] ===== Completeness check finished =====
[2023-06-19 00:53:44,842] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:53:44,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018657585.1_ASM1865758v1_genomic.fna/markers.fasta)
[2023-06-19 00:53:44,843] [INFO] Task started: Blastn
[2023-06-19 00:53:44,844] [INFO] Running command: blastn -query GCA_018657585.1_ASM1865758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5728dfb1-4ad8-4201-8b4a-8ef70c0964ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_018657585.1_ASM1865758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:53:45,542] [INFO] Task succeeded: Blastn
[2023-06-19 00:53:45,547] [INFO] Selected 15 target genomes.
[2023-06-19 00:53:45,548] [INFO] Target genome list was writen to GCA_018657585.1_ASM1865758v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:53:45,558] [INFO] Task started: fastANI
[2023-06-19 00:53:45,558] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb8a07a3-9625-444a-bcad-9be260293538/GCA_018657585.1_ASM1865758v1_genomic.fna.gz --refList GCA_018657585.1_ASM1865758v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018657585.1_ASM1865758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:53:50,923] [INFO] Task succeeded: fastANI
[2023-06-19 00:53:50,939] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:53:50,939] [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_018657585.1	s__GCA-002718515 sp018657585	100.0	509	516	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018701395.1	s__GCA-002718515 sp018701395	77.7526	104	516	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.63	99.41	0.94	0.92	4	-
GCA_014238785.1	s__GCA-002718515 sp014238785	77.5164	91	516	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665385.1	s__GCA-002718515 sp018665385	77.3485	132	516	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.09	99.03	0.85	0.83	4	-
GCA_014381555.1	s__GCA-002718515 sp014381555	77.3373	117	516	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.84	99.84	0.86	0.86	2	-
GCA_012965315.1	s__GCA-002718515 sp012965315	77.0458	87	516	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.71	99.67	0.87	0.85	4	-
GCA_002689385.1	s__GCA-002718515 sp002689385	77.0133	89	516	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381385.1	s__GCA-002718515 sp014381385	76.7041	73	516	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:53:50,942] [INFO] GTDB search result was written to GCA_018657585.1_ASM1865758v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:53:50,943] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:53:50,948] [INFO] DFAST_QC result json was written to GCA_018657585.1_ASM1865758v1_genomic.fna/dqc_result.json
[2023-06-19 00:53:50,948] [INFO] DFAST_QC completed!
[2023-06-19 00:53:50,948] [INFO] Total running time: 0h0m40s