[2024-01-25 18:13:35,523] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:35,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:35,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg3babafff-83ad-420e-a14e-0efbe76d1b24/dqc_reference
[2024-01-25 18:13:36,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:36,801] [INFO] Task started: Prodigal
[2024-01-25 18:13:36,801] [INFO] Running command: gunzip -c /var/lib/cwl/stgf41769bc-8e2d-4dbf-8ec9-bbb70f227e14/GCF_012163145.1_ASM1216314v1_genomic.fna.gz | prodigal -d GCF_012163145.1_ASM1216314v1_genomic.fna/cds.fna -a GCF_012163145.1_ASM1216314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:54,386] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:54,386] [INFO] Task started: HMMsearch
[2024-01-25 18:13:54,386] [INFO] Running command: hmmsearch --tblout GCF_012163145.1_ASM1216314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3babafff-83ad-420e-a14e-0efbe76d1b24/dqc_reference/reference_markers.hmm GCF_012163145.1_ASM1216314v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:54,656] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:54,658] [INFO] Found 6/6 markers.
[2024-01-25 18:13:54,707] [INFO] Query marker FASTA was written to GCF_012163145.1_ASM1216314v1_genomic.fna/markers.fasta
[2024-01-25 18:13:54,707] [INFO] Task started: Blastn
[2024-01-25 18:13:54,707] [INFO] Running command: blastn -query GCF_012163145.1_ASM1216314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3babafff-83ad-420e-a14e-0efbe76d1b24/dqc_reference/reference_markers.fasta -out GCF_012163145.1_ASM1216314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:55,457] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:55,460] [INFO] Selected 22 target genomes.
[2024-01-25 18:13:55,460] [INFO] Target genome list was writen to GCF_012163145.1_ASM1216314v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:55,472] [INFO] Task started: fastANI
[2024-01-25 18:13:55,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgf41769bc-8e2d-4dbf-8ec9-bbb70f227e14/GCF_012163145.1_ASM1216314v1_genomic.fna.gz --refList GCF_012163145.1_ASM1216314v1_genomic.fna/target_genomes.txt --output GCF_012163145.1_ASM1216314v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:23,795] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:23,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3babafff-83ad-420e-a14e-0efbe76d1b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:23,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3babafff-83ad-420e-a14e-0efbe76d1b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:23,813] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:14:23,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:23,814] [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 frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	100.0	2017	2018	95	conclusive
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	87.7806	1497	2018	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	86.6662	1411	2018	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	79.3237	801	2018	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	79.1898	848	2018	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.1783	734	2018	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	79.0665	779	2018	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	79.0324	857	2018	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	78.9681	885	2018	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	78.8332	880	2018	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	78.7934	829	2018	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	78.6618	767	2018	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.5647	719	2018	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.487	818	2018	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	78.4691	743	2018	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.4519	708	2018	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.3915	660	2018	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.3126	747	2018	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	78.2516	730	2018	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	75.5992	259	2018	95	below_threshold
Pyramidobacter piscolens	strain=W5455	GCA_000177335.1	638849	638849	type	True	74.7709	55	2018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:23,815] [INFO] DFAST Taxonomy check result was written to GCF_012163145.1_ASM1216314v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:23,816] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:23,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:23,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3babafff-83ad-420e-a14e-0efbe76d1b24/dqc_reference/checkm_data
[2024-01-25 18:14:23,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:23,873] [INFO] Task started: CheckM
[2024-01-25 18:14:23,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012163145.1_ASM1216314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012163145.1_ASM1216314v1_genomic.fna/checkm_input GCF_012163145.1_ASM1216314v1_genomic.fna/checkm_result
[2024-01-25 18:16:01,753] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:01,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:01,779] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:01,779] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:01,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012163145.1_ASM1216314v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:01,781] [INFO] Task started: Blastn
[2024-01-25 18:16:01,781] [INFO] Running command: blastn -query GCF_012163145.1_ASM1216314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3babafff-83ad-420e-a14e-0efbe76d1b24/dqc_reference/reference_markers_gtdb.fasta -out GCF_012163145.1_ASM1216314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:03,209] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:03,213] [INFO] Selected 13 target genomes.
[2024-01-25 18:16:03,213] [INFO] Target genome list was writen to GCF_012163145.1_ASM1216314v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:03,226] [INFO] Task started: fastANI
[2024-01-25 18:16:03,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgf41769bc-8e2d-4dbf-8ec9-bbb70f227e14/GCF_012163145.1_ASM1216314v1_genomic.fna.gz --refList GCF_012163145.1_ASM1216314v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012163145.1_ASM1216314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:22,615] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:22,624] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:22,624] [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_012163145.1	s__Roseomonas_A frigidaquae	100.0	2017	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_019024325.1	s__Roseomonas_A tokyonensis	87.7455	1501	2018	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_019029495.1	s__Roseomonas_A sp019029495	87.1674	1439	2018	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_012103215.1	s__Roseomonas_A sp012103215	86.7105	1404	2018	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	82.7771	1315	2018	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_011040385.1	s__Roseomonas_A sp011040385	82.566	1292	2018	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_900114315.1	s__Roseomonas_A stagni	82.2599	1293	2018	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	80.8226	1121	2018	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_012163135.1	s__Roseomonas_B oryzicola	79.0318	855	2018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903879915.1	s__UBA9959 sp903879915	74.8039	83	2018	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	99.89	99.83	0.96	0.95	7	-
GCF_000177335.1	s__Pyramidobacter piscolens	74.7785	54	2018	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	98.74	98.74	0.86	0.86	2	-
GCA_016207645.1	s__UBA9959 sp016207645	74.7226	74	2018	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__UBA9959;g__UBA9959	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007215.1	s__Pyramidobacter sp002007215	74.7185	60	2018	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	97.07	95.83	0.85	0.81	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:22,626] [INFO] GTDB search result was written to GCF_012163145.1_ASM1216314v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:22,627] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:22,632] [INFO] DFAST_QC result json was written to GCF_012163145.1_ASM1216314v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:22,636] [INFO] DFAST_QC completed!
[2024-01-25 18:16:22,636] [INFO] Total running time: 0h2m47s