[2024-01-24 10:58:17,122] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:17,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:17,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e56569e-877b-4136-9b77-6268faee9f8f/dqc_reference
[2024-01-24 10:58:18,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:18,310] [INFO] Task started: Prodigal
[2024-01-24 10:58:18,311] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf8dc1c1-b8ac-45b5-93d4-4fd5eb236595/GCF_014050225.1_ASM1405022v1_genomic.fna.gz | prodigal -d GCF_014050225.1_ASM1405022v1_genomic.fna/cds.fna -a GCF_014050225.1_ASM1405022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:30,736] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:30,736] [INFO] Task started: HMMsearch
[2024-01-24 10:58:30,736] [INFO] Running command: hmmsearch --tblout GCF_014050225.1_ASM1405022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e56569e-877b-4136-9b77-6268faee9f8f/dqc_reference/reference_markers.hmm GCF_014050225.1_ASM1405022v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:31,009] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:31,011] [INFO] Found 6/6 markers.
[2024-01-24 10:58:31,057] [INFO] Query marker FASTA was written to GCF_014050225.1_ASM1405022v1_genomic.fna/markers.fasta
[2024-01-24 10:58:31,058] [INFO] Task started: Blastn
[2024-01-24 10:58:31,058] [INFO] Running command: blastn -query GCF_014050225.1_ASM1405022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e56569e-877b-4136-9b77-6268faee9f8f/dqc_reference/reference_markers.fasta -out GCF_014050225.1_ASM1405022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:32,045] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:32,048] [INFO] Selected 19 target genomes.
[2024-01-24 10:58:32,048] [INFO] Target genome list was writen to GCF_014050225.1_ASM1405022v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:32,056] [INFO] Task started: fastANI
[2024-01-24 10:58:32,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf8dc1c1-b8ac-45b5-93d4-4fd5eb236595/GCF_014050225.1_ASM1405022v1_genomic.fna.gz --refList GCF_014050225.1_ASM1405022v1_genomic.fna/target_genomes.txt --output GCF_014050225.1_ASM1405022v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:48,176] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:48,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e56569e-877b-4136-9b77-6268faee9f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:48,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e56569e-877b-4136-9b77-6268faee9f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:48,196] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:48,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:48,197] [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
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	100.0	1417	1432	95	conclusive
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	78.8639	542	1432	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	78.8487	557	1432	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	78.8274	550	1432	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	78.6675	433	1432	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	78.4487	441	1432	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	78.3749	434	1432	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	78.365	442	1432	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	78.3158	450	1432	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	78.3142	449	1432	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.022	380	1432	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.021	339	1432	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.969	331	1432	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.9137	377	1432	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.7888	383	1432	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.5764	314	1432	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	77.551	249	1432	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	77.3563	279	1432	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.3606	129	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:48,199] [INFO] DFAST Taxonomy check result was written to GCF_014050225.1_ASM1405022v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:48,199] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:48,199] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:48,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e56569e-877b-4136-9b77-6268faee9f8f/dqc_reference/checkm_data
[2024-01-24 10:58:48,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:48,240] [INFO] Task started: CheckM
[2024-01-24 10:58:48,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014050225.1_ASM1405022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014050225.1_ASM1405022v1_genomic.fna/checkm_input GCF_014050225.1_ASM1405022v1_genomic.fna/checkm_result
[2024-01-24 10:59:26,556] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:26,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:26,579] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:26,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:26,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014050225.1_ASM1405022v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:26,580] [INFO] Task started: Blastn
[2024-01-24 10:59:26,580] [INFO] Running command: blastn -query GCF_014050225.1_ASM1405022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e56569e-877b-4136-9b77-6268faee9f8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014050225.1_ASM1405022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:28,535] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:28,540] [INFO] Selected 15 target genomes.
[2024-01-24 10:59:28,541] [INFO] Target genome list was writen to GCF_014050225.1_ASM1405022v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:28,559] [INFO] Task started: fastANI
[2024-01-24 10:59:28,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf8dc1c1-b8ac-45b5-93d4-4fd5eb236595/GCF_014050225.1_ASM1405022v1_genomic.fna.gz --refList GCF_014050225.1_ASM1405022v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014050225.1_ASM1405022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:43,282] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:43,295] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:43,295] [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_014050225.1	s__Hongsoonwoonella albiluteola	100.0	1419	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009826895.1	s__Hongsoonwoonella sp009826895	79.6415	717	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	79.5769	643	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_009789575.1	s__Stappia indica_A	79.5128	659	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696535.1	s__Stappia indica	79.3892	632	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_003610575.1	s__Stappia sp003610575	79.3849	608	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_000192745.1	s__Polymorphum gilvum	79.2125	547	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266695.1	s__Hongsoonwoonella zoysiae	79.2076	648	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709505.1	s__Stappia sp002709505	79.0933	482	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423705.1	s__Stappia stellulata	78.9011	555	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008477545.1	s__Roseibium aestuarii	78.3749	434	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113065.1	s__Aureimonas phyllosphaerae	77.4228	250	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_003583935.1	s__Aureimonas flava	77.3581	278	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018987265.1	s__Rhizobium sp018987265	77.2821	265	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193695.1	s__Rhizobium sp014193695	76.9357	274	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.81	98.81	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:43,297] [INFO] GTDB search result was written to GCF_014050225.1_ASM1405022v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:43,297] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:43,301] [INFO] DFAST_QC result json was written to GCF_014050225.1_ASM1405022v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:43,301] [INFO] DFAST_QC completed!
[2024-01-24 10:59:43,302] [INFO] Total running time: 0h1m26s