[2024-01-24 14:05:01,023] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:01,025] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:01,025] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb10ee2d-a863-4ef1-8cdb-35a5ebb535f8/dqc_reference
[2024-01-24 14:05:02,194] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:02,195] [INFO] Task started: Prodigal
[2024-01-24 14:05:02,195] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd443e63-459e-428e-bbec-4cc487ab3a7d/GCF_003253705.1_ASM325370v1_genomic.fna.gz | prodigal -d GCF_003253705.1_ASM325370v1_genomic.fna/cds.fna -a GCF_003253705.1_ASM325370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:16,642] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:16,643] [INFO] Task started: HMMsearch
[2024-01-24 14:05:16,643] [INFO] Running command: hmmsearch --tblout GCF_003253705.1_ASM325370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb10ee2d-a863-4ef1-8cdb-35a5ebb535f8/dqc_reference/reference_markers.hmm GCF_003253705.1_ASM325370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:16,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:16,875] [INFO] Found 6/6 markers.
[2024-01-24 14:05:16,914] [INFO] Query marker FASTA was written to GCF_003253705.1_ASM325370v1_genomic.fna/markers.fasta
[2024-01-24 14:05:16,915] [INFO] Task started: Blastn
[2024-01-24 14:05:16,915] [INFO] Running command: blastn -query GCF_003253705.1_ASM325370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb10ee2d-a863-4ef1-8cdb-35a5ebb535f8/dqc_reference/reference_markers.fasta -out GCF_003253705.1_ASM325370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:17,744] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:17,747] [INFO] Selected 20 target genomes.
[2024-01-24 14:05:17,748] [INFO] Target genome list was writen to GCF_003253705.1_ASM325370v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:17,757] [INFO] Task started: fastANI
[2024-01-24 14:05:17,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd443e63-459e-428e-bbec-4cc487ab3a7d/GCF_003253705.1_ASM325370v1_genomic.fna.gz --refList GCF_003253705.1_ASM325370v1_genomic.fna/target_genomes.txt --output GCF_003253705.1_ASM325370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:38,327] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:38,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb10ee2d-a863-4ef1-8cdb-35a5ebb535f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:38,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb10ee2d-a863-4ef1-8cdb-35a5ebb535f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:38,343] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:38,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:38,344] [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
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	79.3881	816	1619	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	79.099	685	1619	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	78.9018	807	1619	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.7934	688	1619	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	78.7793	654	1619	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	78.7161	646	1619	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	78.7067	690	1619	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	78.6883	700	1619	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	78.6191	763	1619	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	78.5433	547	1619	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.5133	548	1619	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.4372	592	1619	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	78.4288	564	1619	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	78.4278	648	1619	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	78.4119	710	1619	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.3063	577	1619	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	78.2652	568	1619	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	78.2586	597	1619	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	78.2334	585	1619	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.1755	582	1619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:38,346] [INFO] DFAST Taxonomy check result was written to GCF_003253705.1_ASM325370v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:38,347] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:38,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:38,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb10ee2d-a863-4ef1-8cdb-35a5ebb535f8/dqc_reference/checkm_data
[2024-01-24 14:05:38,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:38,394] [INFO] Task started: CheckM
[2024-01-24 14:05:38,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003253705.1_ASM325370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003253705.1_ASM325370v1_genomic.fna/checkm_input GCF_003253705.1_ASM325370v1_genomic.fna/checkm_result
[2024-01-24 14:06:55,715] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:55,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:55,734] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:55,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:55,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003253705.1_ASM325370v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:55,735] [INFO] Task started: Blastn
[2024-01-24 14:06:55,735] [INFO] Running command: blastn -query GCF_003253705.1_ASM325370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb10ee2d-a863-4ef1-8cdb-35a5ebb535f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003253705.1_ASM325370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:57,320] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:57,327] [INFO] Selected 25 target genomes.
[2024-01-24 14:06:57,327] [INFO] Target genome list was writen to GCF_003253705.1_ASM325370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:57,357] [INFO] Task started: fastANI
[2024-01-24 14:06:57,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd443e63-459e-428e-bbec-4cc487ab3a7d/GCF_003253705.1_ASM325370v1_genomic.fna.gz --refList GCF_003253705.1_ASM325370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003253705.1_ASM325370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:24,614] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:24,635] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:24,635] [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_003253705.1	s__Humitalea rosea	100.0	1616	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Humitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000164635.1	s__Roseomonas cervicalis	79.0974	685	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982615.1	s__Roseomonas deserti	78.8333	681	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	78.7761	655	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_014283215.1	s__Siccirubricoccus deserti	78.7344	686	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002631185.1	s__Roseomonas rhizosphaerae	78.6833	651	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706185.1	s__Roseomonas sp902706185	78.6584	735	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343615.1	s__Paracraurococcus sp004343615	78.6474	712	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644535.1	s__Roseomonas_B lacus	78.621	764	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107285.1	s__Roseomonas sp016107285	78.5827	595	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008360935.1	s__Siccirubricoccus phaeus	78.5526	763	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222755.1	s__Roseomonas_B sp005222755	78.5521	671	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490445.1	s__Roseomonas ludipueritiae	78.5318	549	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813355.1	s__Roseomonas_B sp017813355	78.5283	686	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222815.1	s__Roseomonas_A sp005222815	78.5084	720	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	78.5039	675	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106015.1	s__Roseomonas_B sp016106015	78.4943	551	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696345.1	s__Roseomonas sp003696345	78.426	649	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004353985.1	s__Paracraurococcus ruber	78.4223	730	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	99.87	99.87	0.95	0.95	2	-
GCF_004761865.1	s__Crenalkalicoccus roseus	78.3547	640	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490485.1	s__Roseomonas aerophila	78.2578	582	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813395.1	s__Roseomonas sp017813395	78.2317	542	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355405.1	s__Roseomonas sp017355405	78.168	582	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009848505.1	s__Roseomonas deserti_A	78.161	539	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438825.1	s__Roseomonas nepalensis	77.8707	590	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:24,637] [INFO] GTDB search result was written to GCF_003253705.1_ASM325370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:24,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:24,643] [INFO] DFAST_QC result json was written to GCF_003253705.1_ASM325370v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:24,643] [INFO] DFAST_QC completed!
[2024-01-24 14:07:24,643] [INFO] Total running time: 0h2m24s