[2023-06-18 20:30:36,708] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:30:36,710] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:30:36,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5311504-0a3c-4051-a585-d6905e420fa1/dqc_reference
[2023-06-18 20:30:38,216] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:30:38,217] [INFO] Task started: Prodigal
[2023-06-18 20:30:38,217] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f257986-535e-4b38-bf63-64ba4afea087/GCA_018240435.1_ASM1824043v1_genomic.fna.gz | prodigal -d GCA_018240435.1_ASM1824043v1_genomic.fna/cds.fna -a GCA_018240435.1_ASM1824043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:30:48,119] [INFO] Task succeeded: Prodigal
[2023-06-18 20:30:48,119] [INFO] Task started: HMMsearch
[2023-06-18 20:30:48,119] [INFO] Running command: hmmsearch --tblout GCA_018240435.1_ASM1824043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5311504-0a3c-4051-a585-d6905e420fa1/dqc_reference/reference_markers.hmm GCA_018240435.1_ASM1824043v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:30:48,326] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:30:48,327] [INFO] Found 6/6 markers.
[2023-06-18 20:30:48,356] [INFO] Query marker FASTA was written to GCA_018240435.1_ASM1824043v1_genomic.fna/markers.fasta
[2023-06-18 20:30:48,356] [INFO] Task started: Blastn
[2023-06-18 20:30:48,356] [INFO] Running command: blastn -query GCA_018240435.1_ASM1824043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5311504-0a3c-4051-a585-d6905e420fa1/dqc_reference/reference_markers.fasta -out GCA_018240435.1_ASM1824043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:49,283] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:49,287] [INFO] Selected 26 target genomes.
[2023-06-18 20:30:49,287] [INFO] Target genome list was writen to GCA_018240435.1_ASM1824043v1_genomic.fna/target_genomes.txt
[2023-06-18 20:30:49,318] [INFO] Task started: fastANI
[2023-06-18 20:30:49,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f257986-535e-4b38-bf63-64ba4afea087/GCA_018240435.1_ASM1824043v1_genomic.fna.gz --refList GCA_018240435.1_ASM1824043v1_genomic.fna/target_genomes.txt --output GCA_018240435.1_ASM1824043v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:31:06,646] [INFO] Task succeeded: fastANI
[2023-06-18 20:31:06,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5311504-0a3c-4051-a585-d6905e420fa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:31:06,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5311504-0a3c-4051-a585-d6905e420fa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:31:06,666] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:31:06,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:31:06,666] [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
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	79.6318	418	1023	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	79.579	430	1023	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	79.3566	445	1023	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	79.2403	399	1023	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	79.2215	415	1023	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	79.1952	419	1023	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	79.1672	431	1023	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	79.1621	404	1023	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	79.1368	370	1023	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	79.1092	379	1023	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	79.0895	435	1023	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	79.0497	377	1023	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	78.9139	395	1023	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	78.8552	408	1023	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	78.8389	468	1023	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	78.8261	396	1023	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	78.7858	399	1023	95	below_threshold
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	78.7802	348	1023	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	78.7115	389	1023	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	78.6422	380	1023	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	78.6375	398	1023	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	78.5739	359	1023	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	78.5695	382	1023	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.472	365	1023	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	78.409	318	1023	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	78.3458	353	1023	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:31:06,676] [INFO] DFAST Taxonomy check result was written to GCA_018240435.1_ASM1824043v1_genomic.fna/tc_result.tsv
[2023-06-18 20:31:06,676] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:31:06,676] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:31:06,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5311504-0a3c-4051-a585-d6905e420fa1/dqc_reference/checkm_data
[2023-06-18 20:31:06,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:31:06,708] [INFO] Task started: CheckM
[2023-06-18 20:31:06,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018240435.1_ASM1824043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018240435.1_ASM1824043v1_genomic.fna/checkm_input GCA_018240435.1_ASM1824043v1_genomic.fna/checkm_result
[2023-06-18 20:31:49,615] [INFO] Task succeeded: CheckM
[2023-06-18 20:31:49,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:31:49,642] [INFO] ===== Completeness check finished =====
[2023-06-18 20:31:49,642] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:31:49,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018240435.1_ASM1824043v1_genomic.fna/markers.fasta)
[2023-06-18 20:31:49,642] [INFO] Task started: Blastn
[2023-06-18 20:31:49,643] [INFO] Running command: blastn -query GCA_018240435.1_ASM1824043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5311504-0a3c-4051-a585-d6905e420fa1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018240435.1_ASM1824043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:31:51,425] [INFO] Task succeeded: Blastn
[2023-06-18 20:31:51,429] [INFO] Selected 14 target genomes.
[2023-06-18 20:31:51,429] [INFO] Target genome list was writen to GCA_018240435.1_ASM1824043v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:31:51,437] [INFO] Task started: fastANI
[2023-06-18 20:31:51,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f257986-535e-4b38-bf63-64ba4afea087/GCA_018240435.1_ASM1824043v1_genomic.fna.gz --refList GCA_018240435.1_ASM1824043v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018240435.1_ASM1824043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:32:01,819] [INFO] Task succeeded: fastANI
[2023-06-18 20:32:01,832] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:32:01,832] [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
GCA_018240435.1	s__SZAS-103 sp018240435	100.0	1018	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018242445.1	s__SZAS-103 sp018242445	83.1032	668	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242485.1	s__SZAS-103 sp018242485	82.859	643	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241125.1	s__SZAS-103 sp018241125	82.2685	651	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	98.25	97.63	0.95	0.94	3	-
GCF_007859325.1	s__Luteimonas marina	79.3332	448	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	78.9078	310	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114355.1	s__Lysobacter sp900114355	78.9072	417	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	78.8558	408	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	78.6779	494	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_013425525.1	s__Luteimonas sp013425525	78.6586	396	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900018785.1	s__Xanthomonas_B massiliensis	78.6317	382	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018406645.1	s__Lysobacter_A helvus	78.5296	338	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000770795.1	s__Lysobacter_A dokdonensis	78.3979	319	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	78.0546	402	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:32:01,836] [INFO] GTDB search result was written to GCA_018240435.1_ASM1824043v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:32:01,837] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:32:01,841] [INFO] DFAST_QC result json was written to GCA_018240435.1_ASM1824043v1_genomic.fna/dqc_result.json
[2023-06-18 20:32:01,841] [INFO] DFAST_QC completed!
[2023-06-18 20:32:01,842] [INFO] Total running time: 0h1m25s