[2024-01-24 13:01:22,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:22,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:22,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg1273e78c-8cfc-4515-ab02-1f176e9a3aa6/dqc_reference
[2024-01-24 13:01:23,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:23,767] [INFO] Task started: Prodigal
[2024-01-24 13:01:23,767] [INFO] Running command: gunzip -c /var/lib/cwl/stga5f07fc5-c286-4f99-afc6-1d410412ca9a/GCF_003385775.1_ASM338577v1_genomic.fna.gz | prodigal -d GCF_003385775.1_ASM338577v1_genomic.fna/cds.fna -a GCF_003385775.1_ASM338577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:32,942] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:32,943] [INFO] Task started: HMMsearch
[2024-01-24 13:01:32,943] [INFO] Running command: hmmsearch --tblout GCF_003385775.1_ASM338577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1273e78c-8cfc-4515-ab02-1f176e9a3aa6/dqc_reference/reference_markers.hmm GCF_003385775.1_ASM338577v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:33,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:33,285] [INFO] Found 6/6 markers.
[2024-01-24 13:01:33,316] [INFO] Query marker FASTA was written to GCF_003385775.1_ASM338577v1_genomic.fna/markers.fasta
[2024-01-24 13:01:33,317] [INFO] Task started: Blastn
[2024-01-24 13:01:33,317] [INFO] Running command: blastn -query GCF_003385775.1_ASM338577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1273e78c-8cfc-4515-ab02-1f176e9a3aa6/dqc_reference/reference_markers.fasta -out GCF_003385775.1_ASM338577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:34,274] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:34,280] [INFO] Selected 20 target genomes.
[2024-01-24 13:01:34,280] [INFO] Target genome list was writen to GCF_003385775.1_ASM338577v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:34,295] [INFO] Task started: fastANI
[2024-01-24 13:01:34,295] [INFO] Running command: fastANI --query /var/lib/cwl/stga5f07fc5-c286-4f99-afc6-1d410412ca9a/GCF_003385775.1_ASM338577v1_genomic.fna.gz --refList GCF_003385775.1_ASM338577v1_genomic.fna/target_genomes.txt --output GCF_003385775.1_ASM338577v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:49,201] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:49,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1273e78c-8cfc-4515-ab02-1f176e9a3aa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:49,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1273e78c-8cfc-4515-ab02-1f176e9a3aa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:49,217] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:49,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:49,218] [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
Parasphingopyxis lamellibrachiae	strain=DSM 26725	GCA_003385775.1	680125	680125	type	True	100.0	976	976	95	conclusive
Parasphingopyxis algicola	strain=JCM 31719	GCA_013378075.1	2026624	2026624	type	True	80.9125	684	976	95	below_threshold
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	79.3653	536	976	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.5392	210	976	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	77.239	141	976	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.2126	176	976	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	77.0664	148	976	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	76.9856	226	976	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	76.9717	153	976	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	76.92	205	976	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	76.9153	185	976	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.9121	187	976	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	76.8684	195	976	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	76.8336	214	976	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.805	187	976	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.8	192	976	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	76.7859	204	976	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	76.7793	150	976	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	76.4421	174	976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:49,220] [INFO] DFAST Taxonomy check result was written to GCF_003385775.1_ASM338577v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:49,220] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:49,221] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:49,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1273e78c-8cfc-4515-ab02-1f176e9a3aa6/dqc_reference/checkm_data
[2024-01-24 13:01:49,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:49,257] [INFO] Task started: CheckM
[2024-01-24 13:01:49,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385775.1_ASM338577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385775.1_ASM338577v1_genomic.fna/checkm_input GCF_003385775.1_ASM338577v1_genomic.fna/checkm_result
[2024-01-24 13:02:19,330] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:19,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:19,355] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:19,355] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:19,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385775.1_ASM338577v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:19,356] [INFO] Task started: Blastn
[2024-01-24 13:02:19,356] [INFO] Running command: blastn -query GCF_003385775.1_ASM338577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1273e78c-8cfc-4515-ab02-1f176e9a3aa6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385775.1_ASM338577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:20,884] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:20,889] [INFO] Selected 10 target genomes.
[2024-01-24 13:02:20,890] [INFO] Target genome list was writen to GCF_003385775.1_ASM338577v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:20,899] [INFO] Task started: fastANI
[2024-01-24 13:02:20,900] [INFO] Running command: fastANI --query /var/lib/cwl/stga5f07fc5-c286-4f99-afc6-1d410412ca9a/GCF_003385775.1_ASM338577v1_genomic.fna.gz --refList GCF_003385775.1_ASM338577v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385775.1_ASM338577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:26,816] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:26,824] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:26,825] [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_003385775.1	s__Parasphingopyxis lamellibrachiae	100.0	976	976	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479515.1	s__Parasphingopyxis sp905479515	82.9397	436	976	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013378075.1	s__Parasphingopyxis algicola	80.9093	685	976	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014237875.1	s__Parasphingopyxis sp014237875	79.3843	533	976	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013378055.1	s__Parasphingopyxis sp013378055	79.1126	512	976	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001755.1	s__Parasphingopyxis sp013001755	78.6918	383	976	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282385.1	s__Sphingorhabdus_B sp002282385	76.4783	74	976	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.98	99.95	0.99	0.98	4	-
GCA_002299195.1	s__Sphingorhabdus_B sp002299195	75.9469	56	976	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255985.1	s__Sphingorhabdus_B sp002255985	75.9326	66	976	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	98.49	98.44	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:26,826] [INFO] GTDB search result was written to GCF_003385775.1_ASM338577v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:26,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:26,830] [INFO] DFAST_QC result json was written to GCF_003385775.1_ASM338577v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:26,830] [INFO] DFAST_QC completed!
[2024-01-24 13:02:26,831] [INFO] Total running time: 0h1m4s