[2024-01-24 11:12:36,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,242] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe187158-a1ec-4539-ac4a-d347f3204a65/dqc_reference
[2024-01-24 11:12:38,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,663] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fba653c-b567-4271-9ae2-e1a202d290e1/GCF_014205735.1_ASM1420573v1_genomic.fna.gz | prodigal -d GCF_014205735.1_ASM1420573v1_genomic.fna/cds.fna -a GCF_014205735.1_ASM1420573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:50,511] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:50,511] [INFO] Task started: HMMsearch
[2024-01-24 11:12:50,511] [INFO] Running command: hmmsearch --tblout GCF_014205735.1_ASM1420573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe187158-a1ec-4539-ac4a-d347f3204a65/dqc_reference/reference_markers.hmm GCF_014205735.1_ASM1420573v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:50,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:50,714] [INFO] Found 6/6 markers.
[2024-01-24 11:12:50,750] [INFO] Query marker FASTA was written to GCF_014205735.1_ASM1420573v1_genomic.fna/markers.fasta
[2024-01-24 11:12:50,750] [INFO] Task started: Blastn
[2024-01-24 11:12:50,750] [INFO] Running command: blastn -query GCF_014205735.1_ASM1420573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe187158-a1ec-4539-ac4a-d347f3204a65/dqc_reference/reference_markers.fasta -out GCF_014205735.1_ASM1420573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:51,571] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:51,575] [INFO] Selected 10 target genomes.
[2024-01-24 11:12:51,575] [INFO] Target genome list was writen to GCF_014205735.1_ASM1420573v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:51,588] [INFO] Task started: fastANI
[2024-01-24 11:12:51,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fba653c-b567-4271-9ae2-e1a202d290e1/GCF_014205735.1_ASM1420573v1_genomic.fna.gz --refList GCF_014205735.1_ASM1420573v1_genomic.fna/target_genomes.txt --output GCF_014205735.1_ASM1420573v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:59,852] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:59,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe187158-a1ec-4539-ac4a-d347f3204a65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:59,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe187158-a1ec-4539-ac4a-d347f3204a65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:59,863] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:12:59,863] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:12:59,863] [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 wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	100.0	1333	1341	95	inconclusive
Sphingobium wenxiniae	strain=CGMCC 1.7748	GCA_007830065.1	595605	595605	type	True	99.9543	1304	1341	95	inconclusive
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	98.6566	1071	1341	95	inconclusive
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	98.5714	1063	1341	95	inconclusive
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	87.7392	793	1341	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.3475	351	1341	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	78.0934	296	1341	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.065	333	1341	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.6798	278	1341	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.6521	313	1341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:59,865] [INFO] DFAST Taxonomy check result was written to GCF_014205735.1_ASM1420573v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:59,865] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:59,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:59,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe187158-a1ec-4539-ac4a-d347f3204a65/dqc_reference/checkm_data
[2024-01-24 11:12:59,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:59,905] [INFO] Task started: CheckM
[2024-01-24 11:12:59,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205735.1_ASM1420573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205735.1_ASM1420573v1_genomic.fna/checkm_input GCF_014205735.1_ASM1420573v1_genomic.fna/checkm_result
[2024-01-24 11:13:35,792] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:35,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:35,810] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:35,810] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:35,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205735.1_ASM1420573v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:35,811] [INFO] Task started: Blastn
[2024-01-24 11:13:35,811] [INFO] Running command: blastn -query GCF_014205735.1_ASM1420573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe187158-a1ec-4539-ac4a-d347f3204a65/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205735.1_ASM1420573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:37,259] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:37,265] [INFO] Selected 9 target genomes.
[2024-01-24 11:13:37,265] [INFO] Target genome list was writen to GCF_014205735.1_ASM1420573v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:37,273] [INFO] Task started: fastANI
[2024-01-24 11:13:37,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fba653c-b567-4271-9ae2-e1a202d290e1/GCF_014205735.1_ASM1420573v1_genomic.fna.gz --refList GCF_014205735.1_ASM1420573v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205735.1_ASM1420573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:45,946] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:45,955] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:45,955] [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_007830065.1	s__Sphingobium wenxiniae	99.9543	1304	1341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.17	98.76	0.86	0.79	4	conclusive
GCF_001456115.1	s__Sphingobium baderi_A	89.1559	803	1341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100475.1	s__Sphingobium faniae	87.814	803	1341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355855.1	s__Sphingobium cloacae	87.7358	793	1341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000264945.2	s__Sphingobium indicum	84.6281	670	1341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	83.6026	665	1341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_001005725.1	s__Sphingobium chungbukense	83.4152	680	1341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_000447205.1	s__Sphingobium ummariense	83.1419	671	1341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822485.1	s__Sphingobium sp013822485	82.0051	468	1341	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 11:13:45,957] [INFO] GTDB search result was written to GCF_014205735.1_ASM1420573v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:45,957] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:45,960] [INFO] DFAST_QC result json was written to GCF_014205735.1_ASM1420573v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:45,960] [INFO] DFAST_QC completed!
[2024-01-24 11:13:45,961] [INFO] Total running time: 0h1m10s