[2024-01-24 13:36:44,372] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:44,373] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:44,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg62b548d3-db0c-4a36-9fc7-a58c1b87ae6b/dqc_reference
[2024-01-24 13:36:45,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:45,656] [INFO] Task started: Prodigal
[2024-01-24 13:36:45,657] [INFO] Running command: gunzip -c /var/lib/cwl/stga66b7a2f-85c4-4420-9f7f-41444ef46821/GCF_014205635.1_ASM1420563v1_genomic.fna.gz | prodigal -d GCF_014205635.1_ASM1420563v1_genomic.fna/cds.fna -a GCF_014205635.1_ASM1420563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:59,325] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:59,325] [INFO] Task started: HMMsearch
[2024-01-24 13:36:59,326] [INFO] Running command: hmmsearch --tblout GCF_014205635.1_ASM1420563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62b548d3-db0c-4a36-9fc7-a58c1b87ae6b/dqc_reference/reference_markers.hmm GCF_014205635.1_ASM1420563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:59,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:59,553] [INFO] Found 6/6 markers.
[2024-01-24 13:36:59,592] [INFO] Query marker FASTA was written to GCF_014205635.1_ASM1420563v1_genomic.fna/markers.fasta
[2024-01-24 13:36:59,593] [INFO] Task started: Blastn
[2024-01-24 13:36:59,593] [INFO] Running command: blastn -query GCF_014205635.1_ASM1420563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62b548d3-db0c-4a36-9fc7-a58c1b87ae6b/dqc_reference/reference_markers.fasta -out GCF_014205635.1_ASM1420563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:00,481] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:00,485] [INFO] Selected 16 target genomes.
[2024-01-24 13:37:00,485] [INFO] Target genome list was writen to GCF_014205635.1_ASM1420563v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:00,489] [INFO] Task started: fastANI
[2024-01-24 13:37:00,489] [INFO] Running command: fastANI --query /var/lib/cwl/stga66b7a2f-85c4-4420-9f7f-41444ef46821/GCF_014205635.1_ASM1420563v1_genomic.fna.gz --refList GCF_014205635.1_ASM1420563v1_genomic.fna/target_genomes.txt --output GCF_014205635.1_ASM1420563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:10,846] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:10,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62b548d3-db0c-4a36-9fc7-a58c1b87ae6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:10,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62b548d3-db0c-4a36-9fc7-a58c1b87ae6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:10,864] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:10,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:10,864] [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
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	100.0	1266	1270	95	conclusive
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	99.6734	1115	1270	95	conclusive
Polymorphobacter fuscus	strain=DSM 105347	GCA_011927825.1	1439888	1439888	type	True	79.2165	491	1270	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009372075.1	1439888	1439888	type	True	79.1431	498	1270	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	79.134	499	1270	95	below_threshold
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	78.9224	356	1270	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	78.8597	432	1270	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	78.6956	394	1270	95	below_threshold
Sandarakinorhabdus limnophila	strain=DSM 17366	GCA_000420765.1	210512	210512	type	True	78.1986	368	1270	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	77.4696	150	1270	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.4177	268	1270	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	77.2985	137	1270	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.1901	293	1270	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	76.7506	278	1270	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	76.6971	238	1270	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	76.6081	254	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:10,866] [INFO] DFAST Taxonomy check result was written to GCF_014205635.1_ASM1420563v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:10,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:10,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:10,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62b548d3-db0c-4a36-9fc7-a58c1b87ae6b/dqc_reference/checkm_data
[2024-01-24 13:37:10,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:10,909] [INFO] Task started: CheckM
[2024-01-24 13:37:10,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205635.1_ASM1420563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205635.1_ASM1420563v1_genomic.fna/checkm_input GCF_014205635.1_ASM1420563v1_genomic.fna/checkm_result
[2024-01-24 13:37:59,828] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:59,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:59,847] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:59,847] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:59,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205635.1_ASM1420563v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:59,848] [INFO] Task started: Blastn
[2024-01-24 13:37:59,848] [INFO] Running command: blastn -query GCF_014205635.1_ASM1420563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62b548d3-db0c-4a36-9fc7-a58c1b87ae6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205635.1_ASM1420563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:01,481] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:01,489] [INFO] Selected 12 target genomes.
[2024-01-24 13:38:01,489] [INFO] Target genome list was writen to GCF_014205635.1_ASM1420563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:01,510] [INFO] Task started: fastANI
[2024-01-24 13:38:01,510] [INFO] Running command: fastANI --query /var/lib/cwl/stga66b7a2f-85c4-4420-9f7f-41444ef46821/GCF_014205635.1_ASM1420563v1_genomic.fna.gz --refList GCF_014205635.1_ASM1420563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205635.1_ASM1420563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:10,037] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:10,048] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:10,048] [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_014205635.1	s__Polymorphobacter multimanifer	100.0	1266	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	99.78	99.78	0.99	0.99	2	conclusive
GCA_003241875.1	s__Polymorphobacter sp003241875	79.7747	562	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001295935.1	s__Polymorphobacter sp001295935	79.2525	469	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927825.1	s__Polymorphobacter fuscus	79.1976	493	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	99.98	99.98	1.00	1.00	3	-
GCA_002256005.1	s__Polymorphobacter sp002256005	79.1477	483	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423025.1	s__Polymorphobacter sp002423025	79.0212	483	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994245.1	s__Sandarakinorhabdus rubra	78.9233	356	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733735.1	s__Sandarakinorhabdus oryzae	78.6701	396	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903939555.1	s__Polymorphobacter sp903939555	78.6645	339	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	98.54	98.06	0.84	0.82	4	-
GCA_013298745.1	s__Polymorphobacter sp013298745	78.5926	307	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097155.1	s__Glacieibacterium frigidum	78.2942	364	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970445.1	s__Sandarakinorhabdus sp018970445	78.1846	416	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:10,050] [INFO] GTDB search result was written to GCF_014205635.1_ASM1420563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:10,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:10,055] [INFO] DFAST_QC result json was written to GCF_014205635.1_ASM1420563v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:10,055] [INFO] DFAST_QC completed!
[2024-01-24 13:38:10,055] [INFO] Total running time: 0h1m26s