[2023-06-13 13:00:46,455] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:00:46,457] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:00:46,457] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f3cb02e-f8ea-468a-ace7-bd57291a2dd0/dqc_reference
[2023-06-13 13:00:47,883] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:00:47,884] [INFO] Task started: Prodigal
[2023-06-13 13:00:47,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg110ad699-ea9a-4e07-a10b-74e442d87dc1/GCA_022564665.1_ASM2256466v1_genomic.fna.gz | prodigal -d GCA_022564665.1_ASM2256466v1_genomic.fna/cds.fna -a GCA_022564665.1_ASM2256466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:00:56,229] [INFO] Task succeeded: Prodigal
[2023-06-13 13:00:56,229] [INFO] Task started: HMMsearch
[2023-06-13 13:00:56,229] [INFO] Running command: hmmsearch --tblout GCA_022564665.1_ASM2256466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f3cb02e-f8ea-468a-ace7-bd57291a2dd0/dqc_reference/reference_markers.hmm GCA_022564665.1_ASM2256466v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:00:56,564] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:00:56,565] [INFO] Found 6/6 markers.
[2023-06-13 13:00:56,606] [INFO] Query marker FASTA was written to GCA_022564665.1_ASM2256466v1_genomic.fna/markers.fasta
[2023-06-13 13:00:56,607] [INFO] Task started: Blastn
[2023-06-13 13:00:56,607] [INFO] Running command: blastn -query GCA_022564665.1_ASM2256466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f3cb02e-f8ea-468a-ace7-bd57291a2dd0/dqc_reference/reference_markers.fasta -out GCA_022564665.1_ASM2256466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:00:57,250] [INFO] Task succeeded: Blastn
[2023-06-13 13:00:57,255] [INFO] Selected 24 target genomes.
[2023-06-13 13:00:57,255] [INFO] Target genome list was writen to GCA_022564665.1_ASM2256466v1_genomic.fna/target_genomes.txt
[2023-06-13 13:00:57,267] [INFO] Task started: fastANI
[2023-06-13 13:00:57,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg110ad699-ea9a-4e07-a10b-74e442d87dc1/GCA_022564665.1_ASM2256466v1_genomic.fna.gz --refList GCA_022564665.1_ASM2256466v1_genomic.fna/target_genomes.txt --output GCA_022564665.1_ASM2256466v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:01:13,512] [INFO] Task succeeded: fastANI
[2023-06-13 13:01:13,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f3cb02e-f8ea-468a-ace7-bd57291a2dd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:01:13,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f3cb02e-f8ea-468a-ace7-bd57291a2dd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:01:13,517] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:01:13,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:01:13,518] [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
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.972	58	907	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.9455	59	907	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:01:13,520] [INFO] DFAST Taxonomy check result was written to GCA_022564665.1_ASM2256466v1_genomic.fna/tc_result.tsv
[2023-06-13 13:01:13,520] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:01:13,521] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:01:13,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f3cb02e-f8ea-468a-ace7-bd57291a2dd0/dqc_reference/checkm_data
[2023-06-13 13:01:13,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:01:13,559] [INFO] Task started: CheckM
[2023-06-13 13:01:13,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022564665.1_ASM2256466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022564665.1_ASM2256466v1_genomic.fna/checkm_input GCA_022564665.1_ASM2256466v1_genomic.fna/checkm_result
[2023-06-13 13:01:42,197] [INFO] Task succeeded: CheckM
[2023-06-13 13:01:42,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:01:42,223] [INFO] ===== Completeness check finished =====
[2023-06-13 13:01:42,223] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:01:42,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022564665.1_ASM2256466v1_genomic.fna/markers.fasta)
[2023-06-13 13:01:42,224] [INFO] Task started: Blastn
[2023-06-13 13:01:42,224] [INFO] Running command: blastn -query GCA_022564665.1_ASM2256466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f3cb02e-f8ea-468a-ace7-bd57291a2dd0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022564665.1_ASM2256466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:01:43,044] [INFO] Task succeeded: Blastn
[2023-06-13 13:01:43,050] [INFO] Selected 28 target genomes.
[2023-06-13 13:01:43,050] [INFO] Target genome list was writen to GCA_022564665.1_ASM2256466v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:01:43,067] [INFO] Task started: fastANI
[2023-06-13 13:01:43,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg110ad699-ea9a-4e07-a10b-74e442d87dc1/GCA_022564665.1_ASM2256466v1_genomic.fna.gz --refList GCA_022564665.1_ASM2256466v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022564665.1_ASM2256466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:01:56,446] [INFO] Task succeeded: fastANI
[2023-06-13 13:01:56,456] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 13:01:56,457] [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_016873275.1	s__VGXO01 sp016873275	76.2363	79	907	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__VGXO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124975.1	s__QWPT01 sp016124975	76.1486	54	907	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003065.1	s__JABDLI01 sp013003065	76.1186	121	907	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__JABDLI01	95.0	99.48	99.44	0.94	0.93	3	-
GCA_016873255.1	s__UBA966 sp016873255	76.0266	60	907	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364485.1	s__UBA854 sp002364485	75.9619	54	907	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.87	99.87	0.97	0.97	2	-
GCA_016125285.1	s__RI-212 sp016125285	75.6743	60	907	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Zrk34;g__RI-212	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:01:56,459] [INFO] GTDB search result was written to GCA_022564665.1_ASM2256466v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:01:56,459] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:01:56,462] [INFO] DFAST_QC result json was written to GCA_022564665.1_ASM2256466v1_genomic.fna/dqc_result.json
[2023-06-13 13:01:56,462] [INFO] DFAST_QC completed!
[2023-06-13 13:01:56,462] [INFO] Total running time: 0h1m10s