[2023-06-29 12:50:37,490] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:50:37,492] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:50:37,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7dcc3ce-22f9-4b95-87bc-d73fcd1d5c97/dqc_reference
[2023-06-29 12:50:38,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:50:38,734] [INFO] Task started: Prodigal
[2023-06-29 12:50:38,734] [INFO] Running command: gunzip -c /var/lib/cwl/stg60ba07eb-64ca-4281-ac8b-c77768385528/GCA_023150645.1_ASM2315064v1_genomic.fna.gz | prodigal -d GCA_023150645.1_ASM2315064v1_genomic.fna/cds.fna -a GCA_023150645.1_ASM2315064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:50:48,271] [INFO] Task succeeded: Prodigal
[2023-06-29 12:50:48,272] [INFO] Task started: HMMsearch
[2023-06-29 12:50:48,272] [INFO] Running command: hmmsearch --tblout GCA_023150645.1_ASM2315064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7dcc3ce-22f9-4b95-87bc-d73fcd1d5c97/dqc_reference/reference_markers.hmm GCA_023150645.1_ASM2315064v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:50:48,518] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:50:48,520] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg60ba07eb-64ca-4281-ac8b-c77768385528/GCA_023150645.1_ASM2315064v1_genomic.fna.gz]
[2023-06-29 12:50:48,554] [INFO] Query marker FASTA was written to GCA_023150645.1_ASM2315064v1_genomic.fna/markers.fasta
[2023-06-29 12:50:48,554] [INFO] Task started: Blastn
[2023-06-29 12:50:48,554] [INFO] Running command: blastn -query GCA_023150645.1_ASM2315064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7dcc3ce-22f9-4b95-87bc-d73fcd1d5c97/dqc_reference/reference_markers.fasta -out GCA_023150645.1_ASM2315064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:50:49,197] [INFO] Task succeeded: Blastn
[2023-06-29 12:50:49,202] [INFO] Selected 25 target genomes.
[2023-06-29 12:50:49,203] [INFO] Target genome list was writen to GCA_023150645.1_ASM2315064v1_genomic.fna/target_genomes.txt
[2023-06-29 12:50:49,235] [INFO] Task started: fastANI
[2023-06-29 12:50:49,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg60ba07eb-64ca-4281-ac8b-c77768385528/GCA_023150645.1_ASM2315064v1_genomic.fna.gz --refList GCA_023150645.1_ASM2315064v1_genomic.fna/target_genomes.txt --output GCA_023150645.1_ASM2315064v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:51:11,579] [INFO] Task succeeded: fastANI
[2023-06-29 12:51:11,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7dcc3ce-22f9-4b95-87bc-d73fcd1d5c97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:51:11,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7dcc3ce-22f9-4b95-87bc-d73fcd1d5c97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:51:11,597] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:51:11,598] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:51:11,598] [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	76.424	61	1020	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.1812	58	1020	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.6045	124	1020	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.5906	122	1020	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.3654	71	1020	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.1897	62	1020	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.1566	120	1020	95	below_threshold
Limnoglobus roseus	strain=PX52	GCA_008254045.1	2598579	2598579	type	True	75.0714	62	1020	95	below_threshold
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	75.0215	60	1020	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.0157	71	1020	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.0146	107	1020	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	74.9376	82	1020	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.885	208	1020	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	74.8738	82	1020	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8455	204	1020	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	74.7878	84	1020	95	below_threshold
Streptomyces gardneri	strain=JCM 4375	GCA_014655085.1	66892	66892	type	True	74.7833	94	1020	95	below_threshold
Streptomyces zinciresistens	strain=K42	GCA_000225525.2	1073330	1073330	type	True	74.7355	87	1020	95	below_threshold
Streptomyces gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	74.7007	95	1020	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:51:11,600] [INFO] DFAST Taxonomy check result was written to GCA_023150645.1_ASM2315064v1_genomic.fna/tc_result.tsv
[2023-06-29 12:51:11,600] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:51:11,600] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:51:11,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7dcc3ce-22f9-4b95-87bc-d73fcd1d5c97/dqc_reference/checkm_data
[2023-06-29 12:51:11,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:51:11,643] [INFO] Task started: CheckM
[2023-06-29 12:51:11,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023150645.1_ASM2315064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023150645.1_ASM2315064v1_genomic.fna/checkm_input GCA_023150645.1_ASM2315064v1_genomic.fna/checkm_result
[2023-06-29 12:51:45,407] [INFO] Task succeeded: CheckM
[2023-06-29 12:51:45,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:51:45,432] [INFO] ===== Completeness check finished =====
[2023-06-29 12:51:45,432] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:51:45,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023150645.1_ASM2315064v1_genomic.fna/markers.fasta)
[2023-06-29 12:51:45,433] [INFO] Task started: Blastn
[2023-06-29 12:51:45,433] [INFO] Running command: blastn -query GCA_023150645.1_ASM2315064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7dcc3ce-22f9-4b95-87bc-d73fcd1d5c97/dqc_reference/reference_markers_gtdb.fasta -out GCA_023150645.1_ASM2315064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:51:46,409] [INFO] Task succeeded: Blastn
[2023-06-29 12:51:46,414] [INFO] Selected 17 target genomes.
[2023-06-29 12:51:46,414] [INFO] Target genome list was writen to GCA_023150645.1_ASM2315064v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:51:46,429] [INFO] Task started: fastANI
[2023-06-29 12:51:46,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg60ba07eb-64ca-4281-ac8b-c77768385528/GCA_023150645.1_ASM2315064v1_genomic.fna.gz --refList GCA_023150645.1_ASM2315064v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023150645.1_ASM2315064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:51:55,953] [INFO] Task succeeded: fastANI
[2023-06-29 12:51:55,979] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:51:55,979] [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_016793195.1	s__JABWBC01 sp016793195	78.6566	190	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242645.1	s__JAFEBO01 sp018242645	78.6475	136	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFEBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794865.1	s__JAEUJB01 sp016794865	78.1114	322	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAEUJB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343715.1	s__UBA2402 sp002343715	77.9492	150	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	96.81	96.81	0.82	0.82	2	-
GCA_013360695.1	s__JABWBC01 sp013360695	77.911	225	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015200025.1	s__UBA2396 sp015200025	77.9091	185	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2396	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360675.1	s__JABWBB01 sp013360675	77.6765	141	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBB01	95.0	95.57	95.57	0.94	0.94	2	-
GCA_002343325.1	s__UBA2396 sp002343325	77.6243	163	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2396	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929885.1	s__UBA2402 sp903929885	77.389	177	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	99.77	99.77	0.95	0.95	2	-
GCA_018242605.1	s__UBA2402 sp018242605	77.1047	177	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405485.1	s__UBA4658 sp002405485	76.9036	128	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA4658	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	76.888	160	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693765.1	s__RECZ01 sp007693765	76.7982	121	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007124345.1	s__SLFH01 sp007124345	76.7833	112	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_009827205.1	s__GCA-2732755 sp009827205	76.7684	55	1020	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_011053195.1	s__GCA-2732755 sp011053195	76.6514	61	1020	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:51:55,982] [INFO] GTDB search result was written to GCA_023150645.1_ASM2315064v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:51:55,982] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:51:55,986] [INFO] DFAST_QC result json was written to GCA_023150645.1_ASM2315064v1_genomic.fna/dqc_result.json
[2023-06-29 12:51:55,987] [INFO] DFAST_QC completed!
[2023-06-29 12:51:55,987] [INFO] Total running time: 0h1m18s