[2023-06-17 00:12:50,113] [INFO] DFAST_QC pipeline started.
[2023-06-17 00:12:50,115] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 00:12:50,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg9238d41c-a217-4762-bed9-430fb0df1a9a/dqc_reference
[2023-06-17 00:12:51,445] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 00:12:51,446] [INFO] Task started: Prodigal
[2023-06-17 00:12:51,446] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e591911-98f5-40ca-b242-92165f841284/GCA_009930425.1_ASM993042v1_genomic.fna.gz | prodigal -d GCA_009930425.1_ASM993042v1_genomic.fna/cds.fna -a GCA_009930425.1_ASM993042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 00:12:58,920] [INFO] Task succeeded: Prodigal
[2023-06-17 00:12:58,920] [INFO] Task started: HMMsearch
[2023-06-17 00:12:58,920] [INFO] Running command: hmmsearch --tblout GCA_009930425.1_ASM993042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9238d41c-a217-4762-bed9-430fb0df1a9a/dqc_reference/reference_markers.hmm GCA_009930425.1_ASM993042v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 00:12:59,187] [INFO] Task succeeded: HMMsearch
[2023-06-17 00:12:59,188] [INFO] Found 6/6 markers.
[2023-06-17 00:12:59,242] [INFO] Query marker FASTA was written to GCA_009930425.1_ASM993042v1_genomic.fna/markers.fasta
[2023-06-17 00:12:59,243] [INFO] Task started: Blastn
[2023-06-17 00:12:59,243] [INFO] Running command: blastn -query GCA_009930425.1_ASM993042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9238d41c-a217-4762-bed9-430fb0df1a9a/dqc_reference/reference_markers.fasta -out GCA_009930425.1_ASM993042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:13:00,271] [INFO] Task succeeded: Blastn
[2023-06-17 00:13:00,276] [INFO] Selected 26 target genomes.
[2023-06-17 00:13:00,277] [INFO] Target genome list was writen to GCA_009930425.1_ASM993042v1_genomic.fna/target_genomes.txt
[2023-06-17 00:13:00,288] [INFO] Task started: fastANI
[2023-06-17 00:13:00,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e591911-98f5-40ca-b242-92165f841284/GCA_009930425.1_ASM993042v1_genomic.fna.gz --refList GCA_009930425.1_ASM993042v1_genomic.fna/target_genomes.txt --output GCA_009930425.1_ASM993042v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 00:13:18,467] [INFO] Task succeeded: fastANI
[2023-06-17 00:13:18,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9238d41c-a217-4762-bed9-430fb0df1a9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 00:13:18,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9238d41c-a217-4762-bed9-430fb0df1a9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 00:13:18,488] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 00:13:18,488] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 00:13:18,489] [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
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	78.4556	216	628	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	78.3639	218	628	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	78.1329	229	628	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	78.0946	220	628	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	78.0574	209	628	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	78.0419	207	628	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	78.0315	219	628	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	78.0007	210	628	95	below_threshold
Cellulomonas citrea	strain=Ao-9	GCA_009829685.1	1909423	1909423	type	True	77.6964	145	628	95	below_threshold
Kytococcus sedentarius	strain=DSM 20547	GCA_000023925.1	1276	1276	type	True	77.668	85	628	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	77.5727	166	628	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	77.5704	170	628	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	77.4903	171	628	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	77.481	187	628	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	77.3908	184	628	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	77.3683	173	628	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	77.3574	191	628	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	77.2993	171	628	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	77.2863	169	628	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.2155	188	628	95	below_threshold
Actinomyces howellii	strain=NCTC11636	GCA_900637165.1	52771	52771	type	True	77.213	130	628	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	77.1933	131	628	95	below_threshold
Actinomyces bowdenii	strain=DSM 15435	GCA_017592395.1	131109	131109	type	True	76.9781	127	628	95	below_threshold
Beutenbergia cavernae	strain=DSM 12333	GCA_000023105.1	84757	84757	type	True	76.9309	180	628	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	76.7608	121	628	95	below_threshold
Streptomyces polyasparticus	strain=TRM66268-LWL	GCA_014493765.1	2767826	2767826	type	True	76.0008	121	628	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 00:13:18,491] [INFO] DFAST Taxonomy check result was written to GCA_009930425.1_ASM993042v1_genomic.fna/tc_result.tsv
[2023-06-17 00:13:18,492] [INFO] ===== Taxonomy check completed =====
[2023-06-17 00:13:18,492] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 00:13:18,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9238d41c-a217-4762-bed9-430fb0df1a9a/dqc_reference/checkm_data
[2023-06-17 00:13:18,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 00:13:18,530] [INFO] Task started: CheckM
[2023-06-17 00:13:18,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009930425.1_ASM993042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009930425.1_ASM993042v1_genomic.fna/checkm_input GCA_009930425.1_ASM993042v1_genomic.fna/checkm_result
[2023-06-17 00:13:47,405] [INFO] Task succeeded: CheckM
[2023-06-17 00:13:47,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.55%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 00:13:47,432] [INFO] ===== Completeness check finished =====
[2023-06-17 00:13:47,432] [INFO] ===== Start GTDB Search =====
[2023-06-17 00:13:47,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009930425.1_ASM993042v1_genomic.fna/markers.fasta)
[2023-06-17 00:13:47,433] [INFO] Task started: Blastn
[2023-06-17 00:13:47,433] [INFO] Running command: blastn -query GCA_009930425.1_ASM993042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9238d41c-a217-4762-bed9-430fb0df1a9a/dqc_reference/reference_markers_gtdb.fasta -out GCA_009930425.1_ASM993042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:13:48,991] [INFO] Task succeeded: Blastn
[2023-06-17 00:13:48,996] [INFO] Selected 14 target genomes.
[2023-06-17 00:13:48,996] [INFO] Target genome list was writen to GCA_009930425.1_ASM993042v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 00:13:49,090] [INFO] Task started: fastANI
[2023-06-17 00:13:49,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e591911-98f5-40ca-b242-92165f841284/GCA_009930425.1_ASM993042v1_genomic.fna.gz --refList GCA_009930425.1_ASM993042v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009930425.1_ASM993042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 00:13:56,888] [INFO] Task succeeded: fastANI
[2023-06-17 00:13:56,900] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 00:13:56,901] [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_009930425.1	s__UBA1383 sp009930425	100.0	615	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__UBA1383	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002304945.1	s__UBA1383 sp002304945	85.6534	435	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__UBA1383	95.0	97.82	97.82	0.77	0.77	2	-
GCA_002305415.1	s__UBA1383 sp002305415	80.7155	355	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__UBA1383	95.0	99.59	99.59	0.88	0.88	2	-
GCA_017882885.1	s__UBA1383 sp017882885	80.2894	296	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__UBA1383	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193175.1	s__Georgenia ruanii	78.3581	219	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	78.2333	203	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006349365.1	s__Oceanitalea sp006349365	78.0942	220	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	99.20	99.20	0.95	0.95	2	-
GCA_014837105.1	s__Oceanitalea sp014837105	78.0075	209	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193135.1	s__Oceanitalea satyanarayanai	77.9956	211	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513625.1	s__JAAZBW01 sp012513625	77.7258	88	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__JAAZBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900199505.1	s__KH17 sp900199505	77.642	132	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__KH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649925.1	s__JAENWO01 sp016649925	77.5543	121	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__JAENWO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900499005.1	s__Pauljensenia culturomici	77.131	115	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002999235.1	s__Actinomyces sp002999235	76.8262	118	628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.35	98.35	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-17 00:13:56,903] [INFO] GTDB search result was written to GCA_009930425.1_ASM993042v1_genomic.fna/result_gtdb.tsv
[2023-06-17 00:13:56,903] [INFO] ===== GTDB Search completed =====
[2023-06-17 00:13:56,908] [INFO] DFAST_QC result json was written to GCA_009930425.1_ASM993042v1_genomic.fna/dqc_result.json
[2023-06-17 00:13:56,908] [INFO] DFAST_QC completed!
[2023-06-17 00:13:56,908] [INFO] Total running time: 0h1m7s