[2023-07-01 01:12:38,195] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:12:38,199] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:12:38,199] [INFO] DQC Reference Directory: /var/lib/cwl/stg46e81de3-24a3-4306-b533-dbd766986c71/dqc_reference
[2023-07-01 01:12:39,656] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:12:39,663] [INFO] Task started: Prodigal
[2023-07-01 01:12:39,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg054d9ccf-4557-42f7-a04d-8d77828ab14d/GCA_016795005.1_ASM1679500v1_genomic.fna.gz | prodigal -d GCA_016795005.1_ASM1679500v1_genomic.fna/cds.fna -a GCA_016795005.1_ASM1679500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:12:48,793] [INFO] Task succeeded: Prodigal
[2023-07-01 01:12:48,793] [INFO] Task started: HMMsearch
[2023-07-01 01:12:48,793] [INFO] Running command: hmmsearch --tblout GCA_016795005.1_ASM1679500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46e81de3-24a3-4306-b533-dbd766986c71/dqc_reference/reference_markers.hmm GCA_016795005.1_ASM1679500v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:12:49,118] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:12:49,119] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg054d9ccf-4557-42f7-a04d-8d77828ab14d/GCA_016795005.1_ASM1679500v1_genomic.fna.gz]
[2023-07-01 01:12:49,159] [INFO] Query marker FASTA was written to GCA_016795005.1_ASM1679500v1_genomic.fna/markers.fasta
[2023-07-01 01:12:49,159] [INFO] Task started: Blastn
[2023-07-01 01:12:49,160] [INFO] Running command: blastn -query GCA_016795005.1_ASM1679500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46e81de3-24a3-4306-b533-dbd766986c71/dqc_reference/reference_markers.fasta -out GCA_016795005.1_ASM1679500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:12:49,926] [INFO] Task succeeded: Blastn
[2023-07-01 01:12:49,930] [INFO] Selected 24 target genomes.
[2023-07-01 01:12:49,931] [INFO] Target genome list was writen to GCA_016795005.1_ASM1679500v1_genomic.fna/target_genomes.txt
[2023-07-01 01:12:49,936] [INFO] Task started: fastANI
[2023-07-01 01:12:49,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg054d9ccf-4557-42f7-a04d-8d77828ab14d/GCA_016795005.1_ASM1679500v1_genomic.fna.gz --refList GCA_016795005.1_ASM1679500v1_genomic.fna/target_genomes.txt --output GCA_016795005.1_ASM1679500v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:13:16,102] [INFO] Task succeeded: fastANI
[2023-07-01 01:13:16,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46e81de3-24a3-4306-b533-dbd766986c71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:13:16,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46e81de3-24a3-4306-b533-dbd766986c71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:13:16,116] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:13:16,117] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:13:16,117] [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	76.0571	63	929	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.88	78	929	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.8769	78	929	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	75.6496	76	929	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.2289	50	929	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.1289	70	929	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.0386	55	929	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.017	80	929	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	74.9867	59	929	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.9566	74	929	95	below_threshold
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	74.9447	50	929	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	74.7378	58	929	95	below_threshold
Streptacidiphilus rugosus	strain=AM-16	GCA_000744655.1	405783	405783	type	True	74.7243	69	929	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	74.695	58	929	95	below_threshold
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	74.6596	66	929	95	below_threshold
Streptomyces xiamenensis	strain=318	GCA_000993785.3	408015	408015	type	True	74.5598	50	929	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:13:16,119] [INFO] DFAST Taxonomy check result was written to GCA_016795005.1_ASM1679500v1_genomic.fna/tc_result.tsv
[2023-07-01 01:13:16,119] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:13:16,120] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:13:16,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46e81de3-24a3-4306-b533-dbd766986c71/dqc_reference/checkm_data
[2023-07-01 01:13:16,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:13:16,157] [INFO] Task started: CheckM
[2023-07-01 01:13:16,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016795005.1_ASM1679500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016795005.1_ASM1679500v1_genomic.fna/checkm_input GCA_016795005.1_ASM1679500v1_genomic.fna/checkm_result
[2023-07-01 01:13:49,272] [INFO] Task succeeded: CheckM
[2023-07-01 01:13:49,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:13:49,296] [INFO] ===== Completeness check finished =====
[2023-07-01 01:13:49,297] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:13:49,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016795005.1_ASM1679500v1_genomic.fna/markers.fasta)
[2023-07-01 01:13:49,297] [INFO] Task started: Blastn
[2023-07-01 01:13:49,297] [INFO] Running command: blastn -query GCA_016795005.1_ASM1679500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46e81de3-24a3-4306-b533-dbd766986c71/dqc_reference/reference_markers_gtdb.fasta -out GCA_016795005.1_ASM1679500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:13:50,143] [INFO] Task succeeded: Blastn
[2023-07-01 01:13:50,148] [INFO] Selected 18 target genomes.
[2023-07-01 01:13:50,148] [INFO] Target genome list was writen to GCA_016795005.1_ASM1679500v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:13:50,155] [INFO] Task started: fastANI
[2023-07-01 01:13:50,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg054d9ccf-4557-42f7-a04d-8d77828ab14d/GCA_016795005.1_ASM1679500v1_genomic.fna.gz --refList GCA_016795005.1_ASM1679500v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016795005.1_ASM1679500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:14:00,061] [INFO] Task succeeded: fastANI
[2023-07-01 01:14:00,079] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:14:00,079] [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_016795005.1	s__JAEUIV01 sp016795005	100.0	917	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAEUIV01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016794925.1	s__JAEUIW01 sp016794925	77.7313	110	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAEUIW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511945.1	s__UBA11155 sp003511945	77.4214	131	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA11155	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742075.1	s__JACVCL01 sp016742075	77.3822	137	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACVCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331335.1	s__DSSA01 sp011331335	77.0348	136	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__DSSA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793195.1	s__JABWBC01 sp016793195	76.8314	106	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379385.1	s__JACMLW01 sp014379385	76.83	81	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACMLW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360695.1	s__JABWBC01 sp013360695	76.8027	109	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699835.1	s__GCA-016699835 sp016699835	76.8023	111	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-016699835	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693725.1	s__REDD01 sp007693725	76.7915	89	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__REDD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822085.1	s__WM-009 sp013822085	76.6972	87	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__WM-009	95.0	99.63	99.61	0.90	0.89	3	-
GCA_002343715.1	s__UBA2402 sp002343715	76.6431	88	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	96.81	96.81	0.82	0.82	2	-
GCA_007693765.1	s__RECZ01 sp007693765	76.5911	121	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	76.4761	104	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242645.1	s__JAFEBO01 sp018242645	76.4115	93	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFEBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360675.1	s__JABWBB01 sp013360675	76.3662	90	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBB01	95.0	95.57	95.57	0.94	0.94	2	-
GCA_018242605.1	s__UBA2402 sp018242605	76.3616	109	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929885.1	s__UBA2402 sp903929885	76.1447	104	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	99.77	99.77	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-07-01 01:14:00,081] [INFO] GTDB search result was written to GCA_016795005.1_ASM1679500v1_genomic.fna/result_gtdb.tsv
[2023-07-01 01:14:00,082] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:14:00,088] [INFO] DFAST_QC result json was written to GCA_016795005.1_ASM1679500v1_genomic.fna/dqc_result.json
[2023-07-01 01:14:00,088] [INFO] DFAST_QC completed!
[2023-07-01 01:14:00,088] [INFO] Total running time: 0h1m22s