[2024-01-24 13:36:32,077] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,080] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa38a66c-2c3a-4aaa-9792-4f4b65618e69/dqc_reference
[2024-01-24 13:36:33,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,433] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg066ae568-f383-4a9e-bf13-875a68e1a412/GCF_020715685.1_ASM2071568v1_genomic.fna.gz | prodigal -d GCF_020715685.1_ASM2071568v1_genomic.fna/cds.fna -a GCF_020715685.1_ASM2071568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:46,275] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:46,276] [INFO] Task started: HMMsearch
[2024-01-24 13:36:46,276] [INFO] Running command: hmmsearch --tblout GCF_020715685.1_ASM2071568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa38a66c-2c3a-4aaa-9792-4f4b65618e69/dqc_reference/reference_markers.hmm GCF_020715685.1_ASM2071568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:46,567] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:46,569] [INFO] Found 6/6 markers.
[2024-01-24 13:36:46,612] [INFO] Query marker FASTA was written to GCF_020715685.1_ASM2071568v1_genomic.fna/markers.fasta
[2024-01-24 13:36:46,612] [INFO] Task started: Blastn
[2024-01-24 13:36:46,612] [INFO] Running command: blastn -query GCF_020715685.1_ASM2071568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa38a66c-2c3a-4aaa-9792-4f4b65618e69/dqc_reference/reference_markers.fasta -out GCF_020715685.1_ASM2071568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:47,564] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:47,568] [INFO] Selected 26 target genomes.
[2024-01-24 13:36:47,568] [INFO] Target genome list was writen to GCF_020715685.1_ASM2071568v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:47,594] [INFO] Task started: fastANI
[2024-01-24 13:36:47,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg066ae568-f383-4a9e-bf13-875a68e1a412/GCF_020715685.1_ASM2071568v1_genomic.fna.gz --refList GCF_020715685.1_ASM2071568v1_genomic.fna/target_genomes.txt --output GCF_020715685.1_ASM2071568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:12,759] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:12,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa38a66c-2c3a-4aaa-9792-4f4b65618e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:12,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa38a66c-2c3a-4aaa-9792-4f4b65618e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:12,779] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:12,779] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:12,779] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.4716	481	1553	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.2233	430	1553	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.8876	324	1553	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.4409	351	1553	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.3398	454	1553	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	75.5976	275	1553	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	75.579	282	1553	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.5123	313	1553	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	75.4362	353	1553	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	75.4277	360	1553	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	75.391	323	1553	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	75.3296	341	1553	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	75.3161	454	1553	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	75.3042	305	1553	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	75.2839	127	1553	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	75.2651	417	1553	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	75.2624	423	1553	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	75.2514	523	1553	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	75.2168	328	1553	95	below_threshold
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	75.1736	296	1553	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_004361965.1	2074	2074	suspected-type	True	75.1706	405	1553	95	below_threshold
Pseudonocardia autotrophica	strain=NBRC 12743	GCA_003945385.1	2074	2074	suspected-type	True	75.158	411	1553	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	75.1545	608	1553	95	below_threshold
Saccharopolyspora terrae	strain=16K309	GCA_004348435.1	2530384	2530384	type	True	75.1443	276	1553	95	below_threshold
Beutenbergia cavernae	strain=DSM 12333	GCA_000023105.1	84757	84757	type	True	75.1231	356	1553	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	75.1219	407	1553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:12,781] [INFO] DFAST Taxonomy check result was written to GCF_020715685.1_ASM2071568v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:12,781] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:12,782] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:12,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa38a66c-2c3a-4aaa-9792-4f4b65618e69/dqc_reference/checkm_data
[2024-01-24 13:37:12,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:12,830] [INFO] Task started: CheckM
[2024-01-24 13:37:12,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020715685.1_ASM2071568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020715685.1_ASM2071568v1_genomic.fna/checkm_input GCF_020715685.1_ASM2071568v1_genomic.fna/checkm_result
[2024-01-24 13:38:42,410] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:42,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:42,432] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:42,432] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:42,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020715685.1_ASM2071568v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:42,433] [INFO] Task started: Blastn
[2024-01-24 13:38:42,433] [INFO] Running command: blastn -query GCF_020715685.1_ASM2071568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa38a66c-2c3a-4aaa-9792-4f4b65618e69/dqc_reference/reference_markers_gtdb.fasta -out GCF_020715685.1_ASM2071568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:43,870] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:43,874] [INFO] Selected 19 target genomes.
[2024-01-24 13:38:43,875] [INFO] Target genome list was writen to GCF_020715685.1_ASM2071568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:43,941] [INFO] Task started: fastANI
[2024-01-24 13:38:43,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg066ae568-f383-4a9e-bf13-875a68e1a412/GCF_020715685.1_ASM2071568v1_genomic.fna.gz --refList GCF_020715685.1_ASM2071568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020715685.1_ASM2071568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:59,147] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:59,173] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:59,173] [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_003962875.1	s__AWTP1-35 sp003962875	82.3671	627	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268735.1	s__AWTP1-35 sp018268735	80.9717	409	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	79.6125	598	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_903941145.1	s__CAJANQ01 sp903941145	79.2742	367	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_903953195.1	s__SXMI01 sp903953195	79.2047	412	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	98.58	98.55	0.81	0.80	3	-
GCA_903873135.1	s__SXMI01 sp903873135	78.7532	485	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.54	99.49	0.91	0.89	9	-
GCA_903930035.1	s__CAJANQ01 sp903930035	78.7177	325	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118345.1	s__SKRR01 sp007118345	78.5612	430	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SKRR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903852755.1	s__SXMI01 sp903852755	78.4126	482	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.71	99.61	0.93	0.92	10	-
GCA_903925745.1	s__SXMI01 sp903925745	78.2256	457	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777415.1	s__SXMI01 sp005777415	78.0823	351	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.41	99.40	0.88	0.87	3	-
GCF_009650215.1	s__Actinomarinicola tropica	77.4874	478	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	77.3685	482	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	76.9923	380	1553	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090055.1	s__Demequina sp002090055	75.4809	102	1553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719335.1	s__Streptomyces sp000719335	75.3182	383	1553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648795.1	s__Streptomyces cinnamonensis	75.3101	379	1553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.18	96.61	0.93	0.87	24	-
GCF_018614135.1	s__Streptomyces sp018614135	75.2646	291	1553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614195.1	s__Streptomyces sp018614195	75.2546	351	1553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:59,175] [INFO] GTDB search result was written to GCF_020715685.1_ASM2071568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:59,176] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:59,180] [INFO] DFAST_QC result json was written to GCF_020715685.1_ASM2071568v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:59,180] [INFO] DFAST_QC completed!
[2024-01-24 13:38:59,180] [INFO] Total running time: 0h2m27s