[2023-06-13 17:55:51,706] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:55:51,708] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:55:51,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg5af6c315-a8f4-4d0b-a5c5-895f351d14c5/dqc_reference
[2023-06-13 17:55:52,978] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:55:52,979] [INFO] Task started: Prodigal
[2023-06-13 17:55:52,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cf5d5d9-86f5-4e2e-8180-83a43d403cf5/GCA_022563015.1_ASM2256301v1_genomic.fna.gz | prodigal -d GCA_022563015.1_ASM2256301v1_genomic.fna/cds.fna -a GCA_022563015.1_ASM2256301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:56:00,914] [INFO] Task succeeded: Prodigal
[2023-06-13 17:56:00,915] [INFO] Task started: HMMsearch
[2023-06-13 17:56:00,915] [INFO] Running command: hmmsearch --tblout GCA_022563015.1_ASM2256301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5af6c315-a8f4-4d0b-a5c5-895f351d14c5/dqc_reference/reference_markers.hmm GCA_022563015.1_ASM2256301v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:56:01,108] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:56:01,110] [INFO] Found 6/6 markers.
[2023-06-13 17:56:01,138] [INFO] Query marker FASTA was written to GCA_022563015.1_ASM2256301v1_genomic.fna/markers.fasta
[2023-06-13 17:56:01,138] [INFO] Task started: Blastn
[2023-06-13 17:56:01,138] [INFO] Running command: blastn -query GCA_022563015.1_ASM2256301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af6c315-a8f4-4d0b-a5c5-895f351d14c5/dqc_reference/reference_markers.fasta -out GCA_022563015.1_ASM2256301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:01,749] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:01,756] [INFO] Selected 25 target genomes.
[2023-06-13 17:56:01,757] [INFO] Target genome list was writen to GCA_022563015.1_ASM2256301v1_genomic.fna/target_genomes.txt
[2023-06-13 17:56:01,765] [INFO] Task started: fastANI
[2023-06-13 17:56:01,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cf5d5d9-86f5-4e2e-8180-83a43d403cf5/GCA_022563015.1_ASM2256301v1_genomic.fna.gz --refList GCA_022563015.1_ASM2256301v1_genomic.fna/target_genomes.txt --output GCA_022563015.1_ASM2256301v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:56:20,272] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:20,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5af6c315-a8f4-4d0b-a5c5-895f351d14c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:56:20,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5af6c315-a8f4-4d0b-a5c5-895f351d14c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:56:20,281] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:56:20,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:56:20,281] [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
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	76.1311	50	794	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.738	72	794	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.7329	72	794	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.2146	52	794	95	below_threshold
Streptacidiphilus carbonis	strain=NBRC 100919	GCA_000787775.1	105422	105422	type	True	74.7963	60	794	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	74.6669	50	794	95	below_threshold
Streptacidiphilus albus	strain=JL83	GCA_000744705.1	105425	105425	type	True	74.589	70	794	95	below_threshold
Streptacidiphilus albus	strain=NBRC 100918	GCA_000787755.1	105425	105425	type	True	74.5873	72	794	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:56:20,283] [INFO] DFAST Taxonomy check result was written to GCA_022563015.1_ASM2256301v1_genomic.fna/tc_result.tsv
[2023-06-13 17:56:20,285] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:56:20,286] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:56:20,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5af6c315-a8f4-4d0b-a5c5-895f351d14c5/dqc_reference/checkm_data
[2023-06-13 17:56:20,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:56:20,320] [INFO] Task started: CheckM
[2023-06-13 17:56:20,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022563015.1_ASM2256301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022563015.1_ASM2256301v1_genomic.fna/checkm_input GCA_022563015.1_ASM2256301v1_genomic.fna/checkm_result
[2023-06-13 17:56:47,921] [INFO] Task succeeded: CheckM
[2023-06-13 17:56:47,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:56:47,941] [INFO] ===== Completeness check finished =====
[2023-06-13 17:56:47,941] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:56:47,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022563015.1_ASM2256301v1_genomic.fna/markers.fasta)
[2023-06-13 17:56:47,941] [INFO] Task started: Blastn
[2023-06-13 17:56:47,942] [INFO] Running command: blastn -query GCA_022563015.1_ASM2256301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af6c315-a8f4-4d0b-a5c5-895f351d14c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_022563015.1_ASM2256301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:48,802] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:48,806] [INFO] Selected 20 target genomes.
[2023-06-13 17:56:48,807] [INFO] Target genome list was writen to GCA_022563015.1_ASM2256301v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:56:48,818] [INFO] Task started: fastANI
[2023-06-13 17:56:48,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cf5d5d9-86f5-4e2e-8180-83a43d403cf5/GCA_022563015.1_ASM2256301v1_genomic.fna.gz --refList GCA_022563015.1_ASM2256301v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022563015.1_ASM2256301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:57:00,122] [INFO] Task succeeded: fastANI
[2023-06-13 17:57:00,137] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 17:57:00,138] [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_014584315.1	s__CAADGN01 sp014584315	77.1179	140	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696545.1	s__CAADGN01 sp900696545	77.0151	124	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	99.87	99.83	0.94	0.92	3	-
GCA_008363215.1	s__J022 sp008363215	76.956	94	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J022	95.0	99.97	99.97	0.97	0.97	2	-
GCA_007124345.1	s__SLFH01 sp007124345	76.9515	95	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_013360675.1	s__JABWBB01 sp013360675	76.7045	99	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBB01	95.0	95.57	95.57	0.94	0.94	2	-
GCA_002429045.1	s__UBA6054 sp002429045	76.6747	102	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742075.1	s__JACVCL01 sp016742075	76.6618	87	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACVCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793195.1	s__JABWBC01 sp016793195	76.6489	110	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	76.6266	123	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696675.1	s__UBA6054 sp003696675	76.6177	90	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360695.1	s__JABWBC01 sp013360695	76.6162	118	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694925.1	s__SLFH01 sp007694925	76.5922	113	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	76.5798	141	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	76.4454	120	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794865.1	s__JAEUJB01 sp016794865	76.3762	78	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAEUJB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693765.1	s__RECZ01 sp007693765	76.373	109	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794945.1	s__JAEUIX01 sp016794945	76.2151	76	794	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAEUIX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 17:57:00,142] [INFO] GTDB search result was written to GCA_022563015.1_ASM2256301v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:57:00,143] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:57:00,148] [INFO] DFAST_QC result json was written to GCA_022563015.1_ASM2256301v1_genomic.fna/dqc_result.json
[2023-06-13 17:57:00,148] [INFO] DFAST_QC completed!
[2023-06-13 17:57:00,148] [INFO] Total running time: 0h1m8s