[2024-01-24 13:56:13,228] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:13,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:13,230] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fe3b80e-0035-4f11-9fae-64d5c644d0b7/dqc_reference
[2024-01-24 13:56:14,534] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,535] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,535] [INFO] Running command: gunzip -c /var/lib/cwl/stga64cb187-163f-489c-9aaa-80059154381a/GCF_009176975.1_ASM917697v1_genomic.fna.gz | prodigal -d GCF_009176975.1_ASM917697v1_genomic.fna/cds.fna -a GCF_009176975.1_ASM917697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:28,478] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:28,478] [INFO] Task started: HMMsearch
[2024-01-24 13:56:28,478] [INFO] Running command: hmmsearch --tblout GCF_009176975.1_ASM917697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fe3b80e-0035-4f11-9fae-64d5c644d0b7/dqc_reference/reference_markers.hmm GCF_009176975.1_ASM917697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:28,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:28,798] [INFO] Found 6/6 markers.
[2024-01-24 13:56:28,851] [INFO] Query marker FASTA was written to GCF_009176975.1_ASM917697v1_genomic.fna/markers.fasta
[2024-01-24 13:56:28,851] [INFO] Task started: Blastn
[2024-01-24 13:56:28,851] [INFO] Running command: blastn -query GCF_009176975.1_ASM917697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fe3b80e-0035-4f11-9fae-64d5c644d0b7/dqc_reference/reference_markers.fasta -out GCF_009176975.1_ASM917697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:29,810] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:29,948] [INFO] Selected 22 target genomes.
[2024-01-24 13:56:29,948] [INFO] Target genome list was writen to GCF_009176975.1_ASM917697v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:29,981] [INFO] Task started: fastANI
[2024-01-24 13:56:29,981] [INFO] Running command: fastANI --query /var/lib/cwl/stga64cb187-163f-489c-9aaa-80059154381a/GCF_009176975.1_ASM917697v1_genomic.fna.gz --refList GCF_009176975.1_ASM917697v1_genomic.fna/target_genomes.txt --output GCF_009176975.1_ASM917697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:51,022] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:51,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fe3b80e-0035-4f11-9fae-64d5c644d0b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:51,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fe3b80e-0035-4f11-9fae-64d5c644d0b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:51,047] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:51,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:51,048] [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
Aureimonas psammosilenae	strain=YIM DR1026	GCA_009176975.1	2495496	2495496	type	True	100.0	1604	1604	95	conclusive
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	82.8041	974	1604	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	81.3707	828	1604	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	80.4256	700	1604	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	80.3693	717	1604	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	79.7042	646	1604	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	79.5403	625	1604	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	79.0304	456	1604	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	78.9783	487	1604	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	78.9417	467	1604	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	78.9244	504	1604	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	78.8715	515	1604	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	78.5452	519	1604	95	below_threshold
Aureimonas altamirensis	strain=DSM 21988	GCA_001463885.1	370622	370622	type	True	78.185	385	1604	95	below_threshold
Aureimonas altamirensis	strain=DSM 21988	GCA_900141975.1	370622	370622	type	True	78.1455	395	1604	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.0729	378	1604	95	below_threshold
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	77.0582	238	1604	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.9904	273	1604	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	76.778	323	1604	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.6069	358	1604	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.5447	309	1604	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.474	300	1604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:51,049] [INFO] DFAST Taxonomy check result was written to GCF_009176975.1_ASM917697v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:51,050] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:51,050] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:51,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fe3b80e-0035-4f11-9fae-64d5c644d0b7/dqc_reference/checkm_data
[2024-01-24 13:56:51,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:51,097] [INFO] Task started: CheckM
[2024-01-24 13:56:51,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009176975.1_ASM917697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009176975.1_ASM917697v1_genomic.fna/checkm_input GCF_009176975.1_ASM917697v1_genomic.fna/checkm_result
[2024-01-24 13:57:34,848] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:34,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:34,879] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:34,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:34,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009176975.1_ASM917697v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:34,880] [INFO] Task started: Blastn
[2024-01-24 13:57:34,880] [INFO] Running command: blastn -query GCF_009176975.1_ASM917697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fe3b80e-0035-4f11-9fae-64d5c644d0b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_009176975.1_ASM917697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:36,629] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:36,635] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:36,635] [INFO] Target genome list was writen to GCF_009176975.1_ASM917697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:36,647] [INFO] Task started: fastANI
[2024-01-24 13:57:36,647] [INFO] Running command: fastANI --query /var/lib/cwl/stga64cb187-163f-489c-9aaa-80059154381a/GCF_009176975.1_ASM917697v1_genomic.fna.gz --refList GCF_009176975.1_ASM917697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009176975.1_ASM917697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:55,314] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:55,334] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:55,334] [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
GCF_009176975.1	s__Aureimonas_A psammosilene	100.0	1604	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014642635.1	s__Aureimonas_A endophytica	82.8118	971	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	81.373	828	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382705.1	s__Aureimonas ureilytica	80.3662	717	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001425485.1	s__Aureimonas_A sp001425485	79.9577	710	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009765365.1	s__VTOM01 sp009765365	79.7652	681	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463745.1	s__Aureimonas sp001463745	79.6967	603	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424685.1	s__Aureimonas_A sp001424685	79.6589	653	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425575.1	s__Leaf443 sp001425575	79.6405	642	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113065.1	s__Aureimonas phyllosphaerae	79.5053	631	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_014643375.1	s__Aureimonas_A glaciei	79.4042	624	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893625.1	s__Mangrovicella endophytica	79.218	553	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mangrovicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	78.4299	468	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380965.1	s__Aureimonas_A sp014380965	78.2439	299	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	77.8897	297	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_014200015.1	s__Aminobacter niigataensis	77.4975	340	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	77.3657	311	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:55,343] [INFO] GTDB search result was written to GCF_009176975.1_ASM917697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:55,343] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:55,348] [INFO] DFAST_QC result json was written to GCF_009176975.1_ASM917697v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:55,348] [INFO] DFAST_QC completed!
[2024-01-24 13:57:55,348] [INFO] Total running time: 0h1m42s