[2024-01-24 15:02:07,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg7af1a2b5-5862-4b6c-971d-ec3dcb889b29/dqc_reference
[2024-01-24 15:02:09,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,599] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg9325ec60-b40d-4ee1-a068-9186efed0570/GCF_001591285.1_ASM159128v1_genomic.fna.gz | prodigal -d GCF_001591285.1_ASM159128v1_genomic.fna/cds.fna -a GCF_001591285.1_ASM159128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:21,472] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:21,472] [INFO] Task started: HMMsearch
[2024-01-24 15:02:21,472] [INFO] Running command: hmmsearch --tblout GCF_001591285.1_ASM159128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7af1a2b5-5862-4b6c-971d-ec3dcb889b29/dqc_reference/reference_markers.hmm GCF_001591285.1_ASM159128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:21,699] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:21,701] [INFO] Found 6/6 markers.
[2024-01-24 15:02:21,744] [INFO] Query marker FASTA was written to GCF_001591285.1_ASM159128v1_genomic.fna/markers.fasta
[2024-01-24 15:02:21,745] [INFO] Task started: Blastn
[2024-01-24 15:02:21,745] [INFO] Running command: blastn -query GCF_001591285.1_ASM159128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7af1a2b5-5862-4b6c-971d-ec3dcb889b29/dqc_reference/reference_markers.fasta -out GCF_001591285.1_ASM159128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:22,674] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:22,678] [INFO] Selected 11 target genomes.
[2024-01-24 15:02:22,678] [INFO] Target genome list was writen to GCF_001591285.1_ASM159128v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:22,683] [INFO] Task started: fastANI
[2024-01-24 15:02:22,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg9325ec60-b40d-4ee1-a068-9186efed0570/GCF_001591285.1_ASM159128v1_genomic.fna.gz --refList GCF_001591285.1_ASM159128v1_genomic.fna/target_genomes.txt --output GCF_001591285.1_ASM159128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:31,730] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:31,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7af1a2b5-5862-4b6c-971d-ec3dcb889b29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:31,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7af1a2b5-5862-4b6c-971d-ec3dcb889b29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:31,741] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:31,741] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:31,741] [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
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	100.0	1343	1352	95	conclusive
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	99.9975	1349	1352	95	conclusive
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	88.3399	794	1352	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	88.2655	785	1352	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	87.6854	746	1352	95	below_threshold
Sphingobium wenxiniae	strain=CGMCC 1.7748	GCA_007830065.1	595605	595605	type	True	87.6083	754	1352	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.3597	353	1352	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.2522	337	1352	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.0692	335	1352	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.0042	362	1352	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.8491	283	1352	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:31,743] [INFO] DFAST Taxonomy check result was written to GCF_001591285.1_ASM159128v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:31,744] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:31,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:31,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7af1a2b5-5862-4b6c-971d-ec3dcb889b29/dqc_reference/checkm_data
[2024-01-24 15:02:31,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:31,790] [INFO] Task started: CheckM
[2024-01-24 15:02:31,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591285.1_ASM159128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591285.1_ASM159128v1_genomic.fna/checkm_input GCF_001591285.1_ASM159128v1_genomic.fna/checkm_result
[2024-01-24 15:03:12,515] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:12,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:12,532] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:12,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:12,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591285.1_ASM159128v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:12,533] [INFO] Task started: Blastn
[2024-01-24 15:03:12,533] [INFO] Running command: blastn -query GCF_001591285.1_ASM159128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7af1a2b5-5862-4b6c-971d-ec3dcb889b29/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591285.1_ASM159128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:14,392] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:14,395] [INFO] Selected 10 target genomes.
[2024-01-24 15:03:14,395] [INFO] Target genome list was writen to GCF_001591285.1_ASM159128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:14,405] [INFO] Task started: fastANI
[2024-01-24 15:03:14,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg9325ec60-b40d-4ee1-a068-9186efed0570/GCF_001591285.1_ASM159128v1_genomic.fna.gz --refList GCF_001591285.1_ASM159128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591285.1_ASM159128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:24,678] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:24,693] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:24,694] [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_002355855.1	s__Sphingobium cloacae	99.9975	1349	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900100475.1	s__Sphingobium faniae	88.2703	803	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830065.1	s__Sphingobium wenxiniae	87.6259	753	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.17	98.76	0.86	0.79	4	-
GCF_001456115.1	s__Sphingobium baderi_A	87.1966	814	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000264945.2	s__Sphingobium indicum	84.5264	666	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_004152845.1	s__Sphingobium fuliginis	83.9622	689	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_001005725.1	s__Sphingobium chungbukense	83.7366	698	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_000445065.1	s__Sphingobium quisquiliarum	83.3347	632	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	-
GCF_000447205.1	s__Sphingobium ummariense	83.3187	653	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720145.1	s__Sphingobium sp009720145	82.8801	673	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:24,698] [INFO] GTDB search result was written to GCF_001591285.1_ASM159128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:24,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:24,710] [INFO] DFAST_QC result json was written to GCF_001591285.1_ASM159128v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:24,711] [INFO] DFAST_QC completed!
[2024-01-24 15:03:24,711] [INFO] Total running time: 0h1m17s