[2024-01-25 19:55:20,718] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:20,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:20,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg30034bc5-e4d0-4dc9-b604-bdffb5354a5c/dqc_reference
[2024-01-25 19:55:21,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:21,917] [INFO] Task started: Prodigal
[2024-01-25 19:55:21,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg25aab0ca-ba7e-486e-ab32-b443c46a7679/GCF_012103215.1_ASM1210321v1_genomic.fna.gz | prodigal -d GCF_012103215.1_ASM1210321v1_genomic.fna/cds.fna -a GCF_012103215.1_ASM1210321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:37,100] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:37,100] [INFO] Task started: HMMsearch
[2024-01-25 19:55:37,100] [INFO] Running command: hmmsearch --tblout GCF_012103215.1_ASM1210321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30034bc5-e4d0-4dc9-b604-bdffb5354a5c/dqc_reference/reference_markers.hmm GCF_012103215.1_ASM1210321v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:37,431] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:37,432] [INFO] Found 6/6 markers.
[2024-01-25 19:55:37,495] [INFO] Query marker FASTA was written to GCF_012103215.1_ASM1210321v1_genomic.fna/markers.fasta
[2024-01-25 19:55:37,497] [INFO] Task started: Blastn
[2024-01-25 19:55:37,497] [INFO] Running command: blastn -query GCF_012103215.1_ASM1210321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30034bc5-e4d0-4dc9-b604-bdffb5354a5c/dqc_reference/reference_markers.fasta -out GCF_012103215.1_ASM1210321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:38,353] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:38,356] [INFO] Selected 16 target genomes.
[2024-01-25 19:55:38,356] [INFO] Target genome list was writen to GCF_012103215.1_ASM1210321v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:38,366] [INFO] Task started: fastANI
[2024-01-25 19:55:38,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg25aab0ca-ba7e-486e-ab32-b443c46a7679/GCF_012103215.1_ASM1210321v1_genomic.fna.gz --refList GCF_012103215.1_ASM1210321v1_genomic.fna/target_genomes.txt --output GCF_012103215.1_ASM1210321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:00,825] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:00,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30034bc5-e4d0-4dc9-b604-bdffb5354a5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:00,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30034bc5-e4d0-4dc9-b604-bdffb5354a5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:00,836] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:56:00,836] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:00,836] [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 selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	100.0	1853	1863	95	conclusive
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	86.6073	1438	1863	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	86.1639	1399	1863	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.4719	710	1863	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	79.2334	853	1863	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	79.2099	865	1863	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	79.1698	857	1863	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	79.0483	877	1863	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	79.0316	844	1863	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.8948	760	1863	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	78.7645	778	1863	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	78.5932	689	1863	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.5788	677	1863	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.4181	654	1863	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.383	766	1863	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	78.3349	740	1863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:00,837] [INFO] DFAST Taxonomy check result was written to GCF_012103215.1_ASM1210321v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:00,838] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:00,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:00,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30034bc5-e4d0-4dc9-b604-bdffb5354a5c/dqc_reference/checkm_data
[2024-01-25 19:56:00,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:00,892] [INFO] Task started: CheckM
[2024-01-25 19:56:00,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012103215.1_ASM1210321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012103215.1_ASM1210321v1_genomic.fna/checkm_input GCF_012103215.1_ASM1210321v1_genomic.fna/checkm_result
[2024-01-25 19:57:56,160] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:56,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:56,179] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:56,179] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:56,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012103215.1_ASM1210321v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:56,180] [INFO] Task started: Blastn
[2024-01-25 19:57:56,180] [INFO] Running command: blastn -query GCF_012103215.1_ASM1210321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30034bc5-e4d0-4dc9-b604-bdffb5354a5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_012103215.1_ASM1210321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:57,839] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:57,842] [INFO] Selected 9 target genomes.
[2024-01-25 19:57:57,842] [INFO] Target genome list was writen to GCF_012103215.1_ASM1210321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:57,862] [INFO] Task started: fastANI
[2024-01-25 19:57:57,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg25aab0ca-ba7e-486e-ab32-b443c46a7679/GCF_012103215.1_ASM1210321v1_genomic.fna.gz --refList GCF_012103215.1_ASM1210321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012103215.1_ASM1210321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:14,389] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:14,396] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:14,396] [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_012103215.1	s__Roseomonas_A sp012103215	100.0	1853	1863	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_012163145.1	s__Roseomonas_A frigidaquae	86.5755	1441	1863	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_019024325.1	s__Roseomonas_A tokyonensis	86.1665	1398	1863	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	85.9911	1348	1863	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	83.0377	1307	1863	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	82.659	1274	1863	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	82.5385	1285	1863	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	81.1471	1137	1863	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	79.2875	817	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:14,397] [INFO] GTDB search result was written to GCF_012103215.1_ASM1210321v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:14,398] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:14,401] [INFO] DFAST_QC result json was written to GCF_012103215.1_ASM1210321v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:14,401] [INFO] DFAST_QC completed!
[2024-01-25 19:58:14,401] [INFO] Total running time: 0h2m54s