[2023-06-29 04:41:50,351] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:41:50,353] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:41:50,354] [INFO] DQC Reference Directory: /var/lib/cwl/stga52545d9-04ba-4115-8ed7-d08f750a9dea/dqc_reference
[2023-06-29 04:41:51,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:41:51,620] [INFO] Task started: Prodigal
[2023-06-29 04:41:51,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a4bfe8f-7082-4b62-8e57-240f4e8c8ec4/GCA_015487775.1_ASM1548777v1_genomic.fna.gz | prodigal -d GCA_015487775.1_ASM1548777v1_genomic.fna/cds.fna -a GCA_015487775.1_ASM1548777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:41:59,781] [INFO] Task succeeded: Prodigal
[2023-06-29 04:41:59,782] [INFO] Task started: HMMsearch
[2023-06-29 04:41:59,782] [INFO] Running command: hmmsearch --tblout GCA_015487775.1_ASM1548777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga52545d9-04ba-4115-8ed7-d08f750a9dea/dqc_reference/reference_markers.hmm GCA_015487775.1_ASM1548777v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:42:00,030] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:42:00,034] [INFO] Found 6/6 markers.
[2023-06-29 04:42:00,072] [INFO] Query marker FASTA was written to GCA_015487775.1_ASM1548777v1_genomic.fna/markers.fasta
[2023-06-29 04:42:00,072] [INFO] Task started: Blastn
[2023-06-29 04:42:00,073] [INFO] Running command: blastn -query GCA_015487775.1_ASM1548777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga52545d9-04ba-4115-8ed7-d08f750a9dea/dqc_reference/reference_markers.fasta -out GCA_015487775.1_ASM1548777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:42:00,731] [INFO] Task succeeded: Blastn
[2023-06-29 04:42:00,735] [INFO] Selected 29 target genomes.
[2023-06-29 04:42:00,735] [INFO] Target genome list was writen to GCA_015487775.1_ASM1548777v1_genomic.fna/target_genomes.txt
[2023-06-29 04:42:00,737] [INFO] Task started: fastANI
[2023-06-29 04:42:00,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4bfe8f-7082-4b62-8e57-240f4e8c8ec4/GCA_015487775.1_ASM1548777v1_genomic.fna.gz --refList GCA_015487775.1_ASM1548777v1_genomic.fna/target_genomes.txt --output GCA_015487775.1_ASM1548777v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:42:21,270] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:21,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga52545d9-04ba-4115-8ed7-d08f750a9dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:42:21,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga52545d9-04ba-4115-8ed7-d08f750a9dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:42:21,283] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:42:21,283] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:42:21,284] [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	76.3315	53	862	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	76.0031	66	862	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.9349	69	862	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.4297	66	862	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.3735	73	862	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:42:21,286] [INFO] DFAST Taxonomy check result was written to GCA_015487775.1_ASM1548777v1_genomic.fna/tc_result.tsv
[2023-06-29 04:42:21,287] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:42:21,287] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:42:21,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga52545d9-04ba-4115-8ed7-d08f750a9dea/dqc_reference/checkm_data
[2023-06-29 04:42:21,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:42:21,326] [INFO] Task started: CheckM
[2023-06-29 04:42:21,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015487775.1_ASM1548777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015487775.1_ASM1548777v1_genomic.fna/checkm_input GCA_015487775.1_ASM1548777v1_genomic.fna/checkm_result
[2023-06-29 04:42:52,989] [INFO] Task succeeded: CheckM
[2023-06-29 04:42:52,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:42:53,011] [INFO] ===== Completeness check finished =====
[2023-06-29 04:42:53,011] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:42:53,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015487775.1_ASM1548777v1_genomic.fna/markers.fasta)
[2023-06-29 04:42:53,012] [INFO] Task started: Blastn
[2023-06-29 04:42:53,012] [INFO] Running command: blastn -query GCA_015487775.1_ASM1548777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga52545d9-04ba-4115-8ed7-d08f750a9dea/dqc_reference/reference_markers_gtdb.fasta -out GCA_015487775.1_ASM1548777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:42:53,977] [INFO] Task succeeded: Blastn
[2023-06-29 04:42:53,981] [INFO] Selected 23 target genomes.
[2023-06-29 04:42:53,982] [INFO] Target genome list was writen to GCA_015487775.1_ASM1548777v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:42:53,987] [INFO] Task started: fastANI
[2023-06-29 04:42:53,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4bfe8f-7082-4b62-8e57-240f4e8c8ec4/GCA_015487775.1_ASM1548777v1_genomic.fna.gz --refList GCA_015487775.1_ASM1548777v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015487775.1_ASM1548777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:43:06,159] [INFO] Task succeeded: fastANI
[2023-06-29 04:43:06,177] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 04:43:06,178] [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_015492715.1	s__S146-42 sp015492715	99.354	689	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__S146-42	95.0	99.50	99.47	0.92	0.91	3	conclusive
GCA_007694925.1	s__SLFH01 sp007694925	77.3674	168	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007124345.1	s__SLFH01 sp007124345	77.2637	149	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_003696675.1	s__UBA6054 sp003696675	77.13	110	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584315.1	s__CAADGN01 sp014584315	77.0929	156	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480345.1	s__UBA1926 sp002480345	77.0353	139	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	76.973	141	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124375.1	s__RI-211 sp016124375	76.9649	73	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RI-211	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696545.1	s__CAADGN01 sp900696545	76.897	140	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	99.87	99.83	0.94	0.92	3	-
GCA_016709445.1	s__PNC22 sp016709445	76.7157	128	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	76.674	112	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_016873295.1	s__VGXM01 sp016873295	76.6452	138	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__VGXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	76.5739	172	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	76.5451	137	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693765.1	s__RECZ01 sp007693765	76.533	108	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337215.1	s__UBA1926 sp002337215	76.4936	131	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053195.1	s__GCA-2732755 sp011053195	76.4738	79	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642965.1	s__UBA1924 sp017642965	76.4426	95	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242605.1	s__UBA2402 sp018242605	76.3308	93	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697045.1	s__J022 sp003697045	76.1186	81	862	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J022	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:43:06,180] [INFO] GTDB search result was written to GCA_015487775.1_ASM1548777v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:43:06,180] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:43:06,184] [INFO] DFAST_QC result json was written to GCA_015487775.1_ASM1548777v1_genomic.fna/dqc_result.json
[2023-06-29 04:43:06,184] [INFO] DFAST_QC completed!
[2023-06-29 04:43:06,184] [INFO] Total running time: 0h1m16s