[2024-01-24 15:02:37,356] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:37,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:37,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e276364-dfbc-44ab-ab3d-7cc2eea06e9d/dqc_reference
[2024-01-24 15:02:38,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,884] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgea5da404-016f-4d95-96f3-b0e89099239b/GCF_002355855.1_ASM235585v1_genomic.fna.gz | prodigal -d GCF_002355855.1_ASM235585v1_genomic.fna/cds.fna -a GCF_002355855.1_ASM235585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:53,810] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:53,810] [INFO] Task started: HMMsearch
[2024-01-24 15:02:53,811] [INFO] Running command: hmmsearch --tblout GCF_002355855.1_ASM235585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e276364-dfbc-44ab-ab3d-7cc2eea06e9d/dqc_reference/reference_markers.hmm GCF_002355855.1_ASM235585v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:54,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:54,117] [INFO] Found 6/6 markers.
[2024-01-24 15:02:54,165] [INFO] Query marker FASTA was written to GCF_002355855.1_ASM235585v1_genomic.fna/markers.fasta
[2024-01-24 15:02:54,166] [INFO] Task started: Blastn
[2024-01-24 15:02:54,166] [INFO] Running command: blastn -query GCF_002355855.1_ASM235585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e276364-dfbc-44ab-ab3d-7cc2eea06e9d/dqc_reference/reference_markers.fasta -out GCF_002355855.1_ASM235585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:55,239] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:55,242] [INFO] Selected 11 target genomes.
[2024-01-24 15:02:55,243] [INFO] Target genome list was writen to GCF_002355855.1_ASM235585v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:55,251] [INFO] Task started: fastANI
[2024-01-24 15:02:55,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgea5da404-016f-4d95-96f3-b0e89099239b/GCF_002355855.1_ASM235585v1_genomic.fna.gz --refList GCF_002355855.1_ASM235585v1_genomic.fna/target_genomes.txt --output GCF_002355855.1_ASM235585v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:06,068] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:06,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e276364-dfbc-44ab-ab3d-7cc2eea06e9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:06,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e276364-dfbc-44ab-ab3d-7cc2eea06e9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:06,079] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:06,080] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:06,080] [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=JCM 10874	GCA_002355855.1	120107	120107	type	True	100.0	1508	1513	95	conclusive
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	99.9032	1342	1513	95	conclusive
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	88.3972	827	1513	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	88.3305	824	1513	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	87.8304	769	1513	95	below_threshold
Sphingobium wenxiniae	strain=CGMCC 1.7748	GCA_007830065.1	595605	595605	type	True	87.7241	775	1513	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.3065	351	1513	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.28	369	1513	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.0955	373	1513	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.0047	350	1513	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.9606	298	1513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:06,081] [INFO] DFAST Taxonomy check result was written to GCF_002355855.1_ASM235585v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:06,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:06,082] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:06,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e276364-dfbc-44ab-ab3d-7cc2eea06e9d/dqc_reference/checkm_data
[2024-01-24 15:03:06,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:06,128] [INFO] Task started: CheckM
[2024-01-24 15:03:06,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002355855.1_ASM235585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002355855.1_ASM235585v1_genomic.fna/checkm_input GCF_002355855.1_ASM235585v1_genomic.fna/checkm_result
[2024-01-24 15:03:51,737] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:51,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:51,765] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:51,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:51,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002355855.1_ASM235585v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:51,766] [INFO] Task started: Blastn
[2024-01-24 15:03:51,766] [INFO] Running command: blastn -query GCF_002355855.1_ASM235585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e276364-dfbc-44ab-ab3d-7cc2eea06e9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002355855.1_ASM235585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:53,728] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:53,731] [INFO] Selected 10 target genomes.
[2024-01-24 15:03:53,732] [INFO] Target genome list was writen to GCF_002355855.1_ASM235585v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:53,739] [INFO] Task started: fastANI
[2024-01-24 15:03:53,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgea5da404-016f-4d95-96f3-b0e89099239b/GCF_002355855.1_ASM235585v1_genomic.fna.gz --refList GCF_002355855.1_ASM235585v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002355855.1_ASM235585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:05,573] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:05,582] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:05,583] [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	100.0	1507	1513	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	88.1866	819	1513	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	87.7252	774	1513	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	87.3537	850	1513	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	84.9331	663	1513	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	83.9671	714	1513	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	83.9564	715	1513	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	83.5033	666	1513	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	83.4076	695	1513	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	83.1414	698	1513	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 15:04:05,584] [INFO] GTDB search result was written to GCF_002355855.1_ASM235585v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:05,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:05,589] [INFO] DFAST_QC result json was written to GCF_002355855.1_ASM235585v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:05,589] [INFO] DFAST_QC completed!
[2024-01-24 15:04:05,589] [INFO] Total running time: 0h1m28s