[2024-01-24 13:09:33,682] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,684] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d94dd0f-6808-49da-9422-ed3d44f920bb/dqc_reference
[2024-01-24 13:09:34,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,001] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b9ee4ec-efff-4d12-8d32-306cf3c4d299/GCF_000420545.1_ASM42054v1_genomic.fna.gz | prodigal -d GCF_000420545.1_ASM42054v1_genomic.fna/cds.fna -a GCF_000420545.1_ASM42054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:44,978] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:44,978] [INFO] Task started: HMMsearch
[2024-01-24 13:09:44,979] [INFO] Running command: hmmsearch --tblout GCF_000420545.1_ASM42054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d94dd0f-6808-49da-9422-ed3d44f920bb/dqc_reference/reference_markers.hmm GCF_000420545.1_ASM42054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:45,272] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:45,273] [INFO] Found 6/6 markers.
[2024-01-24 13:09:45,302] [INFO] Query marker FASTA was written to GCF_000420545.1_ASM42054v1_genomic.fna/markers.fasta
[2024-01-24 13:09:45,303] [INFO] Task started: Blastn
[2024-01-24 13:09:45,303] [INFO] Running command: blastn -query GCF_000420545.1_ASM42054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d94dd0f-6808-49da-9422-ed3d44f920bb/dqc_reference/reference_markers.fasta -out GCF_000420545.1_ASM42054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:46,246] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:46,249] [INFO] Selected 15 target genomes.
[2024-01-24 13:09:46,250] [INFO] Target genome list was writen to GCF_000420545.1_ASM42054v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:46,256] [INFO] Task started: fastANI
[2024-01-24 13:09:46,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b9ee4ec-efff-4d12-8d32-306cf3c4d299/GCF_000420545.1_ASM42054v1_genomic.fna.gz --refList GCF_000420545.1_ASM42054v1_genomic.fna/target_genomes.txt --output GCF_000420545.1_ASM42054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:56,530] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:56,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d94dd0f-6808-49da-9422-ed3d44f920bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:56,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d94dd0f-6808-49da-9422-ed3d44f920bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:56,545] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:09:56,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:56,546] [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
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	100.0	1015	1016	95	conclusive
Arenimonas oryziterrae	strain=YC6267	GCA_000747135.1	498055	498055	type	True	99.9933	1008	1016	95	conclusive
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	80.695	584	1016	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	80.6637	484	1016	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	80.3475	499	1016	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	80.0323	493	1016	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	79.939	513	1016	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	79.8546	512	1016	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	79.3452	443	1016	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	79.2279	462	1016	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	79.0438	421	1016	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	78.7099	341	1016	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	78.6403	333	1016	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	78.601	355	1016	95	below_threshold
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	78.4894	396	1016	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:56,547] [INFO] DFAST Taxonomy check result was written to GCF_000420545.1_ASM42054v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:56,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:56,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:56,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d94dd0f-6808-49da-9422-ed3d44f920bb/dqc_reference/checkm_data
[2024-01-24 13:09:56,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:56,583] [INFO] Task started: CheckM
[2024-01-24 13:09:56,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420545.1_ASM42054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420545.1_ASM42054v1_genomic.fna/checkm_input GCF_000420545.1_ASM42054v1_genomic.fna/checkm_result
[2024-01-24 13:10:27,655] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:27,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:27,672] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:27,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:27,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420545.1_ASM42054v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:27,673] [INFO] Task started: Blastn
[2024-01-24 13:10:27,674] [INFO] Running command: blastn -query GCF_000420545.1_ASM42054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d94dd0f-6808-49da-9422-ed3d44f920bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420545.1_ASM42054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:29,478] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:29,481] [INFO] Selected 18 target genomes.
[2024-01-24 13:10:29,481] [INFO] Target genome list was writen to GCF_000420545.1_ASM42054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:29,512] [INFO] Task started: fastANI
[2024-01-24 13:10:29,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b9ee4ec-efff-4d12-8d32-306cf3c4d299/GCF_000420545.1_ASM42054v1_genomic.fna.gz --refList GCF_000420545.1_ASM42054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420545.1_ASM42054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:41,662] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:41,676] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:41,677] [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_000420545.1	s__Arenimonas oryziterrae	100.0	1016	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_006265115.1	s__Arenimonas terrae	80.7056	583	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747075.1	s__Arenimonas malthae	80.6938	481	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993735.1	s__Arenimonas daejeonensis	80.5404	527	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747155.1	s__Arenimonas metalli	80.4384	540	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724815.1	s__Arenimonas sp001724815	80.3482	507	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	80.3122	502	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743535.1	s__Arenimonas donghaensis	80.0169	494	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801685.1	s__Arenimonas sp001801685	80.0014	476	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426365.1	s__Arenimonas composti	79.9341	513	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.98	99.98	1.00	1.00	2	-
GCA_003241895.1	s__Arenimonas sp003241895	79.849	482	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638745.1	s__Arenimonas maotaiensis	79.5289	374	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442535.1	s__Lysobacter antibioticus	79.269	457	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.45	98.45	0.94	0.94	2	-
GCF_000731095.1	s__Lysobacter antibioticus_B	79.2326	458	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586305.1	s__Lysobacter tabacisoli	79.1586	433	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	79.0533	485	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_000336385.2	s__Lysobacter antibioticus_A	78.997	442	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211765.1	s__Pseudoxanthomonas kaohsiungensis	78.4792	397	1016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:41,678] [INFO] GTDB search result was written to GCF_000420545.1_ASM42054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:41,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:41,683] [INFO] DFAST_QC result json was written to GCF_000420545.1_ASM42054v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:41,683] [INFO] DFAST_QC completed!
[2024-01-24 13:10:41,683] [INFO] Total running time: 0h1m8s