[2024-01-24 11:13:04,630] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,633] [INFO] DQC Reference Directory: /var/lib/cwl/stgca322586-f1cd-44ba-b395-62812fbc0e12/dqc_reference
[2024-01-24 11:13:05,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,842] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f119dfb-2133-4112-ba72-a88b18587fcf/GCF_018129085.1_ASM1812908v1_genomic.fna.gz | prodigal -d GCF_018129085.1_ASM1812908v1_genomic.fna/cds.fna -a GCF_018129085.1_ASM1812908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:26,559] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:26,560] [INFO] Task started: HMMsearch
[2024-01-24 11:13:26,560] [INFO] Running command: hmmsearch --tblout GCF_018129085.1_ASM1812908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca322586-f1cd-44ba-b395-62812fbc0e12/dqc_reference/reference_markers.hmm GCF_018129085.1_ASM1812908v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:26,961] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:26,962] [INFO] Found 6/6 markers.
[2024-01-24 11:13:27,020] [INFO] Query marker FASTA was written to GCF_018129085.1_ASM1812908v1_genomic.fna/markers.fasta
[2024-01-24 11:13:27,021] [INFO] Task started: Blastn
[2024-01-24 11:13:27,021] [INFO] Running command: blastn -query GCF_018129085.1_ASM1812908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca322586-f1cd-44ba-b395-62812fbc0e12/dqc_reference/reference_markers.fasta -out GCF_018129085.1_ASM1812908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:27,900] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:27,905] [INFO] Selected 20 target genomes.
[2024-01-24 11:13:27,906] [INFO] Target genome list was writen to GCF_018129085.1_ASM1812908v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:27,914] [INFO] Task started: fastANI
[2024-01-24 11:13:27,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f119dfb-2133-4112-ba72-a88b18587fcf/GCF_018129085.1_ASM1812908v1_genomic.fna.gz --refList GCF_018129085.1_ASM1812908v1_genomic.fna/target_genomes.txt --output GCF_018129085.1_ASM1812908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:54,013] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:54,013] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca322586-f1cd-44ba-b395-62812fbc0e12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:54,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca322586-f1cd-44ba-b395-62812fbc0e12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:54,032] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:54,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:54,033] [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
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	100.0	2339	2346	95	conclusive
Roseomonas arctica	strain=LMG 28251	GCA_018128965.1	1509237	1509237	type	True	80.3141	933	2346	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	79.703	904	2346	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.6976	705	2346	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	79.6942	813	2346	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	79.413	943	2346	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	79.2495	870	2346	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	79.2187	878	2346	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	79.1906	879	2346	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	79.1057	738	2346	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	79.1057	850	2346	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	79.0149	823	2346	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	79.0123	885	2346	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	78.979	892	2346	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	78.8497	865	2346	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.8422	726	2346	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	78.6341	682	2346	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.5963	683	2346	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.5132	645	2346	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.1728	667	2346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:54,034] [INFO] DFAST Taxonomy check result was written to GCF_018129085.1_ASM1812908v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:54,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:54,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:54,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca322586-f1cd-44ba-b395-62812fbc0e12/dqc_reference/checkm_data
[2024-01-24 11:13:54,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:54,106] [INFO] Task started: CheckM
[2024-01-24 11:13:54,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018129085.1_ASM1812908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018129085.1_ASM1812908v1_genomic.fna/checkm_input GCF_018129085.1_ASM1812908v1_genomic.fna/checkm_result
[2024-01-24 11:15:02,260] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:02,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:02,288] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:02,288] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:02,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018129085.1_ASM1812908v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:02,289] [INFO] Task started: Blastn
[2024-01-24 11:15:02,289] [INFO] Running command: blastn -query GCF_018129085.1_ASM1812908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca322586-f1cd-44ba-b395-62812fbc0e12/dqc_reference/reference_markers_gtdb.fasta -out GCF_018129085.1_ASM1812908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:03,912] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:03,916] [INFO] Selected 22 target genomes.
[2024-01-24 11:15:03,917] [INFO] Target genome list was writen to GCF_018129085.1_ASM1812908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:03,935] [INFO] Task started: fastANI
[2024-01-24 11:15:03,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f119dfb-2133-4112-ba72-a88b18587fcf/GCF_018129085.1_ASM1812908v1_genomic.fna.gz --refList GCF_018129085.1_ASM1812908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018129085.1_ASM1812908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:34,049] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:34,074] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:34,074] [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_018129085.1	s__Roseomonas_C hellenica	100.0	2339	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_C	95.0	97.71	97.71	0.92	0.92	2	conclusive
GCF_018128965.1	s__Roseomonas_C arctica	80.3506	926	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	79.8681	827	2346	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_018129005.1	s__Roseomonas_B eburnea	79.7893	963	2346	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_012163135.1	s__Roseomonas_B oryzicola	79.7423	898	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017813355.1	s__Roseomonas_B sp017813355	79.7355	883	2346	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	79.6646	711	2346	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_012927745.1	s__Roseomonas_B sp012927745	79.541	910	2346	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_013112485.1	s__Paracraurococcus sp013112485	79.4465	946	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	79.4268	886	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775475.1	s__Belnapia sp016775475	79.3941	948	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805545.1	s__Belnapia sp902805545	79.3851	781	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	79.2992	783	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014283215.1	s__Siccirubricoccus deserti	79.2131	876	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005222755.1	s__Roseomonas_B sp005222755	79.1902	890	2346	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_900101615.1	s__Belnapia rosea	79.1879	880	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	98.36	98.36	0.89	0.89	2	-
GCF_014644455.1	s__Caldovatus sediminis	79.1695	838	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173615.1	s__Roseomonas_A sp003173615	79.1289	862	2346	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_008360935.1	s__Siccirubricoccus phaeus	79.0569	980	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012103215.1	s__Roseomonas_A sp012103215	78.8928	856	2346	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_005222815.1	s__Roseomonas_A sp005222815	78.8878	879	2346	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_016805305.1	s__Roseomonas_A sp016805305	78.7979	958	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:34,076] [INFO] GTDB search result was written to GCF_018129085.1_ASM1812908v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:34,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:34,081] [INFO] DFAST_QC result json was written to GCF_018129085.1_ASM1812908v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:34,081] [INFO] DFAST_QC completed!
[2024-01-24 11:15:34,082] [INFO] Total running time: 0h2m29s