[2024-01-24 13:17:47,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:47,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:47,144] [INFO] DQC Reference Directory: /var/lib/cwl/stgab733420-8137-4ec1-8279-3f0cf322c4d2/dqc_reference
[2024-01-24 13:17:48,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:48,482] [INFO] Task started: Prodigal
[2024-01-24 13:17:48,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg1015d7c3-46b8-4138-94d8-73894da923da/GCF_003034225.1_ASM303422v1_genomic.fna.gz | prodigal -d GCF_003034225.1_ASM303422v1_genomic.fna/cds.fna -a GCF_003034225.1_ASM303422v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:01,979] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:01,979] [INFO] Task started: HMMsearch
[2024-01-24 13:18:01,979] [INFO] Running command: hmmsearch --tblout GCF_003034225.1_ASM303422v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab733420-8137-4ec1-8279-3f0cf322c4d2/dqc_reference/reference_markers.hmm GCF_003034225.1_ASM303422v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:02,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:02,317] [INFO] Found 6/6 markers.
[2024-01-24 13:18:02,358] [INFO] Query marker FASTA was written to GCF_003034225.1_ASM303422v1_genomic.fna/markers.fasta
[2024-01-24 13:18:02,358] [INFO] Task started: Blastn
[2024-01-24 13:18:02,359] [INFO] Running command: blastn -query GCF_003034225.1_ASM303422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab733420-8137-4ec1-8279-3f0cf322c4d2/dqc_reference/reference_markers.fasta -out GCF_003034225.1_ASM303422v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:03,504] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:03,507] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:03,508] [INFO] Target genome list was writen to GCF_003034225.1_ASM303422v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:03,515] [INFO] Task started: fastANI
[2024-01-24 13:18:03,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg1015d7c3-46b8-4138-94d8-73894da923da/GCF_003034225.1_ASM303422v1_genomic.fna.gz --refList GCF_003034225.1_ASM303422v1_genomic.fna/target_genomes.txt --output GCF_003034225.1_ASM303422v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:20,644] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:20,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab733420-8137-4ec1-8279-3f0cf322c4d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:20,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab733420-8137-4ec1-8279-3f0cf322c4d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:20,659] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:20,659] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:20,660] [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
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	100.0	1451	1454	95	conclusive
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	84.0348	831	1454	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	80.7171	617	1454	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	80.6231	515	1454	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	80.2708	606	1454	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	80.1309	591	1454	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	79.6516	536	1454	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	79.5249	622	1454	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	79.4527	620	1454	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	79.375	552	1454	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	79.2489	467	1454	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	79.1287	469	1454	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	79.0064	477	1454	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	78.9002	480	1454	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	78.592	372	1454	95	below_threshold
Sphingomonas prati	strain=CGMCC 1.15645	GCA_014643515.1	1843237	1843237	type	True	78.4758	436	1454	95	below_threshold
Sphingomonas prati	strain=W18RD	GCA_009755805.1	1843237	1843237	type	True	78.4499	435	1454	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	78.4065	437	1454	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:20,661] [INFO] DFAST Taxonomy check result was written to GCF_003034225.1_ASM303422v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:20,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:20,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:20,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab733420-8137-4ec1-8279-3f0cf322c4d2/dqc_reference/checkm_data
[2024-01-24 13:18:20,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:20,720] [INFO] Task started: CheckM
[2024-01-24 13:18:20,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003034225.1_ASM303422v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003034225.1_ASM303422v1_genomic.fna/checkm_input GCF_003034225.1_ASM303422v1_genomic.fna/checkm_result
[2024-01-24 13:19:03,956] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:03,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:03,982] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:03,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:03,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003034225.1_ASM303422v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:03,983] [INFO] Task started: Blastn
[2024-01-24 13:19:03,983] [INFO] Running command: blastn -query GCF_003034225.1_ASM303422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab733420-8137-4ec1-8279-3f0cf322c4d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003034225.1_ASM303422v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:06,026] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:06,030] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:06,030] [INFO] Target genome list was writen to GCF_003034225.1_ASM303422v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:06,049] [INFO] Task started: fastANI
[2024-01-24 13:19:06,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg1015d7c3-46b8-4138-94d8-73894da923da/GCF_003034225.1_ASM303422v1_genomic.fna.gz --refList GCF_003034225.1_ASM303422v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003034225.1_ASM303422v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:19,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:19,314] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:19,315] [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_003034225.1	s__Sphingomonas_E fennica	100.0	1451	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	conclusive
GCF_900188165.1	s__Sphingomonas_E laterariae	84.0445	830	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002151445.1	s__Sphingomonas_E sp002151445	82.203	742	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	80.6401	514	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	80.0827	665	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_000383095.1	s__Sphingomonas_N sp000383095	79.8614	534	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	79.5857	543	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	79.5229	623	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274695.1	s__Rhizorhabdus montanisoli	79.4932	497	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	79.4781	619	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001015195.1	s__Rhizorhabdus sp001015195	79.4207	560	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	79.007	346	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	78.9349	431	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643515.1	s__Sphingomonas_G prati	78.4721	436	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:19,330] [INFO] GTDB search result was written to GCF_003034225.1_ASM303422v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:19,331] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:19,338] [INFO] DFAST_QC result json was written to GCF_003034225.1_ASM303422v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:19,339] [INFO] DFAST_QC completed!
[2024-01-24 13:19:19,339] [INFO] Total running time: 0h1m32s