[2024-01-24 12:13:43,057] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:43,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:43,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg18bd5891-e582-4a78-a407-bb28fd3e87b5/dqc_reference
[2024-01-24 12:13:44,517] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:44,518] [INFO] Task started: Prodigal
[2024-01-24 12:13:44,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg94f5807c-341f-4899-92dc-41dffaeb044b/GCF_011090165.1_ASM1109016v1_genomic.fna.gz | prodigal -d GCF_011090165.1_ASM1109016v1_genomic.fna/cds.fna -a GCF_011090165.1_ASM1109016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:06,725] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:06,725] [INFO] Task started: HMMsearch
[2024-01-24 12:14:06,725] [INFO] Running command: hmmsearch --tblout GCF_011090165.1_ASM1109016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18bd5891-e582-4a78-a407-bb28fd3e87b5/dqc_reference/reference_markers.hmm GCF_011090165.1_ASM1109016v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:07,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:07,102] [INFO] Found 6/6 markers.
[2024-01-24 12:14:07,161] [INFO] Query marker FASTA was written to GCF_011090165.1_ASM1109016v1_genomic.fna/markers.fasta
[2024-01-24 12:14:07,161] [INFO] Task started: Blastn
[2024-01-24 12:14:07,161] [INFO] Running command: blastn -query GCF_011090165.1_ASM1109016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18bd5891-e582-4a78-a407-bb28fd3e87b5/dqc_reference/reference_markers.fasta -out GCF_011090165.1_ASM1109016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:08,303] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:08,307] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:08,308] [INFO] Target genome list was writen to GCF_011090165.1_ASM1109016v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:08,314] [INFO] Task started: fastANI
[2024-01-24 12:14:08,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg94f5807c-341f-4899-92dc-41dffaeb044b/GCF_011090165.1_ASM1109016v1_genomic.fna.gz --refList GCF_011090165.1_ASM1109016v1_genomic.fna/target_genomes.txt --output GCF_011090165.1_ASM1109016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:35,939] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:35,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18bd5891-e582-4a78-a407-bb28fd3e87b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:35,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18bd5891-e582-4a78-a407-bb28fd3e87b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:35,954] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:35,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:35,954] [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
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	100.0	2279	2281	95	conclusive
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	87.0936	1552	2281	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	86.9669	1543	2281	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	86.737	1601	2281	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	86.6159	1599	2281	95	below_threshold
Duganella levis	strain=CY42W	GCA_009857605.1	2692169	2692169	type	True	85.727	1545	2281	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	85.6158	1513	2281	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	85.5716	1356	2281	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	85.5336	1538	2281	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	85.4398	1571	2281	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	83.5916	1309	2281	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	83.3862	1181	2281	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	83.1423	1160	2281	95	below_threshold
Janthinobacterium agaricidamnosum	strain=DSM 9628	GCA_000723165.1	55508	55508	type	True	81.3467	1040	2281	95	below_threshold
Janthinobacterium agaricidamnosum	strain=NBRC 102515	GCA_001571185.1	55508	55508	type	True	81.3363	1028	2281	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:35,956] [INFO] DFAST Taxonomy check result was written to GCF_011090165.1_ASM1109016v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:35,957] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:35,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:35,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18bd5891-e582-4a78-a407-bb28fd3e87b5/dqc_reference/checkm_data
[2024-01-24 12:14:35,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:36,026] [INFO] Task started: CheckM
[2024-01-24 12:14:36,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011090165.1_ASM1109016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011090165.1_ASM1109016v1_genomic.fna/checkm_input GCF_011090165.1_ASM1109016v1_genomic.fna/checkm_result
[2024-01-24 12:15:37,848] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:37,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:37,882] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:37,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:37,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011090165.1_ASM1109016v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:37,883] [INFO] Task started: Blastn
[2024-01-24 12:15:37,883] [INFO] Running command: blastn -query GCF_011090165.1_ASM1109016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18bd5891-e582-4a78-a407-bb28fd3e87b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_011090165.1_ASM1109016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:40,050] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:40,053] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:40,053] [INFO] Target genome list was writen to GCF_011090165.1_ASM1109016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:40,065] [INFO] Task started: fastANI
[2024-01-24 12:15:40,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg94f5807c-341f-4899-92dc-41dffaeb044b/GCF_011090165.1_ASM1109016v1_genomic.fna.gz --refList GCF_011090165.1_ASM1109016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011090165.1_ASM1109016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:05,048] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:05,064] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:05,064] [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_011090165.1	s__Duganella aceris	100.0	2279	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013375995.1	s__Duganella sp013375995	87.4205	1624	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000381565.1	s__Duganella sp000381565	87.2448	1511	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_000335815.1	s__Duganella sp000335815	87.2249	1555	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.81	95.66	0.89	0.89	4	-
GCF_003416985.1	s__Duganella sp003416985	87.2191	1545	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.63	95.41	0.92	0.79	7	-
GCF_003416895.1	s__Duganella sp003416895	87.079	1578	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	99.92	99.92	0.99	0.99	2	-
GCF_009380215.1	s__Duganella sp009380215	86.9365	1546	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674565.1	s__Duganella rivi	86.6949	1607	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	N/A	N/A	N/A	N/A	1	-
GCF_009674495.1	s__Duganella alba	86.6698	1591	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
GCF_013408245.1	s__Duganella sp013408245	86.1177	1572	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110275.1	s__Duganella sp900110275	86.0897	1612	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833525.1	s__Duganella sp017833525	86.0854	1611	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614165.1	s__Duganella callida	85.6162	1512	2281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:05,067] [INFO] GTDB search result was written to GCF_011090165.1_ASM1109016v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:05,067] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:05,071] [INFO] DFAST_QC result json was written to GCF_011090165.1_ASM1109016v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:05,071] [INFO] DFAST_QC completed!
[2024-01-24 12:16:05,071] [INFO] Total running time: 0h2m22s