[2024-01-24 13:49:18,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:18,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:18,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg2eedf275-0969-4a49-80c7-85d49fed60a2/dqc_reference
[2024-01-24 13:49:19,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:19,637] [INFO] Task started: Prodigal
[2024-01-24 13:49:19,637] [INFO] Running command: gunzip -c /var/lib/cwl/stgd36d52ad-0fc6-4c3d-ae76-1dc936f03858/GCF_000420645.1_ASM42064v1_genomic.fna.gz | prodigal -d GCF_000420645.1_ASM42064v1_genomic.fna/cds.fna -a GCF_000420645.1_ASM42064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:33,059] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:33,059] [INFO] Task started: HMMsearch
[2024-01-24 13:49:33,059] [INFO] Running command: hmmsearch --tblout GCF_000420645.1_ASM42064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2eedf275-0969-4a49-80c7-85d49fed60a2/dqc_reference/reference_markers.hmm GCF_000420645.1_ASM42064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:33,376] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:33,377] [INFO] Found 6/6 markers.
[2024-01-24 13:49:33,419] [INFO] Query marker FASTA was written to GCF_000420645.1_ASM42064v1_genomic.fna/markers.fasta
[2024-01-24 13:49:33,419] [INFO] Task started: Blastn
[2024-01-24 13:49:33,419] [INFO] Running command: blastn -query GCF_000420645.1_ASM42064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2eedf275-0969-4a49-80c7-85d49fed60a2/dqc_reference/reference_markers.fasta -out GCF_000420645.1_ASM42064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:34,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:34,420] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:34,420] [INFO] Target genome list was writen to GCF_000420645.1_ASM42064v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:34,427] [INFO] Task started: fastANI
[2024-01-24 13:49:34,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgd36d52ad-0fc6-4c3d-ae76-1dc936f03858/GCF_000420645.1_ASM42064v1_genomic.fna.gz --refList GCF_000420645.1_ASM42064v1_genomic.fna/target_genomes.txt --output GCF_000420645.1_ASM42064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:50,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:50,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2eedf275-0969-4a49-80c7-85d49fed60a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:50,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2eedf275-0969-4a49-80c7-85d49fed60a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:50,037] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:50,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:50,038] [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
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	100.0	1496	1498	95	conclusive
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	78.5799	476	1498	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	78.5133	519	1498	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	78.4722	495	1498	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	78.3833	515	1498	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	78.262	487	1498	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	77.996	411	1498	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	76.7654	181	1498	95	below_threshold
Arenimonas oryziterrae	strain=YC6267	GCA_000747135.1	498055	498055	type	True	76.6171	150	1498	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.5799	144	1498	95	below_threshold
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	76.5742	152	1498	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	76.5038	247	1498	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.4736	233	1498	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	76.4036	215	1498	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	76.3872	155	1498	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.2773	164	1498	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	76.2331	243	1498	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	76.0622	167	1498	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	75.9784	167	1498	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	75.8883	174	1498	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:50,039] [INFO] DFAST Taxonomy check result was written to GCF_000420645.1_ASM42064v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:50,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:50,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:50,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2eedf275-0969-4a49-80c7-85d49fed60a2/dqc_reference/checkm_data
[2024-01-24 13:49:50,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:50,083] [INFO] Task started: CheckM
[2024-01-24 13:49:50,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420645.1_ASM42064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420645.1_ASM42064v1_genomic.fna/checkm_input GCF_000420645.1_ASM42064v1_genomic.fna/checkm_result
[2024-01-24 13:50:37,083] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:37,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:37,100] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:37,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:37,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420645.1_ASM42064v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:37,101] [INFO] Task started: Blastn
[2024-01-24 13:50:37,101] [INFO] Running command: blastn -query GCF_000420645.1_ASM42064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2eedf275-0969-4a49-80c7-85d49fed60a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420645.1_ASM42064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:38,933] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:38,936] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:38,936] [INFO] Target genome list was writen to GCF_000420645.1_ASM42064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:38,947] [INFO] Task started: fastANI
[2024-01-24 13:50:38,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgd36d52ad-0fc6-4c3d-ae76-1dc936f03858/GCF_000420645.1_ASM42064v1_genomic.fna.gz --refList GCF_000420645.1_ASM42064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420645.1_ASM42064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:50,713] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:50,723] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:50,724] [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_000420645.1	s__Nevskia ramosa	100.0	1496	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903885465.1	s__Nevskia sp903885465	92.1535	1042	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823855.1	s__Nevskia sp013823855	83.988	907	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711955.1	s__Nevskia soli	78.5161	519	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	78.4573	497	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	78.4306	413	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822975.1	s__Nevskia sp903822975	78.3885	471	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000426685.1	s__Solimonas flava	78.3392	521	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	78.2977	483	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297005.1	s__Stagnimonas sp004297005	78.0937	355	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
GCA_903970595.1	s__Nevskia sp903970595	77.9148	350	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970615.1	s__Nevskia sp903970615	77.78	332	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	76.2158	244	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:50,725] [INFO] GTDB search result was written to GCF_000420645.1_ASM42064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:50,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:50,729] [INFO] DFAST_QC result json was written to GCF_000420645.1_ASM42064v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:50,729] [INFO] DFAST_QC completed!
[2024-01-24 13:50:50,729] [INFO] Total running time: 0h1m32s