[2024-01-24 11:26:38,433] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,435] [INFO] DQC Reference Directory: /var/lib/cwl/stga72d4a55-32da-48c1-b3d8-e2d458fa35a2/dqc_reference
[2024-01-24 11:26:39,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:39,824] [INFO] Task started: Prodigal
[2024-01-24 11:26:39,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b3b9f2e-866d-41d7-aecb-a6eac5c1e6ae/GCF_019029495.1_ASM1902949v1_genomic.fna.gz | prodigal -d GCF_019029495.1_ASM1902949v1_genomic.fna/cds.fna -a GCF_019029495.1_ASM1902949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:57,084] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:57,085] [INFO] Task started: HMMsearch
[2024-01-24 11:26:57,085] [INFO] Running command: hmmsearch --tblout GCF_019029495.1_ASM1902949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga72d4a55-32da-48c1-b3d8-e2d458fa35a2/dqc_reference/reference_markers.hmm GCF_019029495.1_ASM1902949v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:57,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:57,399] [INFO] Found 6/6 markers.
[2024-01-24 11:26:57,455] [INFO] Query marker FASTA was written to GCF_019029495.1_ASM1902949v1_genomic.fna/markers.fasta
[2024-01-24 11:26:57,455] [INFO] Task started: Blastn
[2024-01-24 11:26:57,455] [INFO] Running command: blastn -query GCF_019029495.1_ASM1902949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga72d4a55-32da-48c1-b3d8-e2d458fa35a2/dqc_reference/reference_markers.fasta -out GCF_019029495.1_ASM1902949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:58,321] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:58,326] [INFO] Selected 17 target genomes.
[2024-01-24 11:26:58,326] [INFO] Target genome list was writen to GCF_019029495.1_ASM1902949v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:58,337] [INFO] Task started: fastANI
[2024-01-24 11:26:58,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b3b9f2e-866d-41d7-aecb-a6eac5c1e6ae/GCF_019029495.1_ASM1902949v1_genomic.fna.gz --refList GCF_019029495.1_ASM1902949v1_genomic.fna/target_genomes.txt --output GCF_019029495.1_ASM1902949v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:20,299] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:20,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga72d4a55-32da-48c1-b3d8-e2d458fa35a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:20,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga72d4a55-32da-48c1-b3d8-e2d458fa35a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:20,312] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:20,313] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:20,313] [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	87.1192	1448	1861	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	87.1058	1409	1861	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	85.948	1359	1861	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.0725	697	1861	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	79.0595	852	1861	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	79.0159	736	1861	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	78.9803	813	1861	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	78.8197	834	1861	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	78.7642	811	1861	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	78.6506	642	1861	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	78.5347	717	1861	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.5044	687	1861	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.3634	665	1861	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	78.3445	697	1861	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	78.2895	716	1861	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.1965	697	1861	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.0396	566	1861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:20,315] [INFO] DFAST Taxonomy check result was written to GCF_019029495.1_ASM1902949v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:20,315] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:20,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:20,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga72d4a55-32da-48c1-b3d8-e2d458fa35a2/dqc_reference/checkm_data
[2024-01-24 11:27:20,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:20,372] [INFO] Task started: CheckM
[2024-01-24 11:27:20,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019029495.1_ASM1902949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019029495.1_ASM1902949v1_genomic.fna/checkm_input GCF_019029495.1_ASM1902949v1_genomic.fna/checkm_result
[2024-01-24 11:28:30,477] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:30,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:30,505] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:30,505] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:30,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019029495.1_ASM1902949v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:30,506] [INFO] Task started: Blastn
[2024-01-24 11:28:30,506] [INFO] Running command: blastn -query GCF_019029495.1_ASM1902949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga72d4a55-32da-48c1-b3d8-e2d458fa35a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_019029495.1_ASM1902949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:32,190] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:32,195] [INFO] Selected 10 target genomes.
[2024-01-24 11:28:32,195] [INFO] Target genome list was writen to GCF_019029495.1_ASM1902949v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:32,232] [INFO] Task started: fastANI
[2024-01-24 11:28:32,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b3b9f2e-866d-41d7-aecb-a6eac5c1e6ae/GCF_019029495.1_ASM1902949v1_genomic.fna.gz --refList GCF_019029495.1_ASM1902949v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019029495.1_ASM1902949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:49,979] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:49,994] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:49,994] [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_019029495.1	s__Roseomonas_A sp019029495	100.0	1861	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019024325.1	s__Roseomonas_A tokyonensis	87.128	1406	1861	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_012163145.1	s__Roseomonas_A frigidaquae	87.1204	1446	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012103215.1	s__Roseomonas_A sp012103215	85.916	1364	1861	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	82.625	1316	1861	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	82.3452	1283	1861	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	82.2549	1260	1861	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_003173615.1	s__Roseomonas_A sp003173615	80.663	1053	1861	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_004761865.1	s__Crenalkalicoccus roseus	78.6335	755	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141905.1	s__Roseomonas rosea	78.3219	700	1861	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 11:28:49,996] [INFO] GTDB search result was written to GCF_019029495.1_ASM1902949v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:49,997] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:50,000] [INFO] DFAST_QC result json was written to GCF_019029495.1_ASM1902949v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:50,000] [INFO] DFAST_QC completed!
[2024-01-24 11:28:50,000] [INFO] Total running time: 0h2m12s