[2024-01-25 18:06:20,806] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:20,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:20,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg37542c67-4e5c-4a8e-82e3-4a9d5bce9b74/dqc_reference
[2024-01-25 18:06:22,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:22,021] [INFO] Task started: Prodigal
[2024-01-25 18:06:22,022] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbaca51f-ab3e-4790-baeb-65d5dd34abc9/GCF_009739515.1_ASM973951v1_genomic.fna.gz | prodigal -d GCF_009739515.1_ASM973951v1_genomic.fna/cds.fna -a GCF_009739515.1_ASM973951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:34,103] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:34,103] [INFO] Task started: HMMsearch
[2024-01-25 18:06:34,103] [INFO] Running command: hmmsearch --tblout GCF_009739515.1_ASM973951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37542c67-4e5c-4a8e-82e3-4a9d5bce9b74/dqc_reference/reference_markers.hmm GCF_009739515.1_ASM973951v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:34,389] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:34,390] [INFO] Found 6/6 markers.
[2024-01-25 18:06:34,445] [INFO] Query marker FASTA was written to GCF_009739515.1_ASM973951v1_genomic.fna/markers.fasta
[2024-01-25 18:06:34,446] [INFO] Task started: Blastn
[2024-01-25 18:06:34,446] [INFO] Running command: blastn -query GCF_009739515.1_ASM973951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37542c67-4e5c-4a8e-82e3-4a9d5bce9b74/dqc_reference/reference_markers.fasta -out GCF_009739515.1_ASM973951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:35,452] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:35,455] [INFO] Selected 20 target genomes.
[2024-01-25 18:06:35,455] [INFO] Target genome list was writen to GCF_009739515.1_ASM973951v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:35,466] [INFO] Task started: fastANI
[2024-01-25 18:06:35,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbaca51f-ab3e-4790-baeb-65d5dd34abc9/GCF_009739515.1_ASM973951v1_genomic.fna.gz --refList GCF_009739515.1_ASM973951v1_genomic.fna/target_genomes.txt --output GCF_009739515.1_ASM973951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:54,713] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:54,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37542c67-4e5c-4a8e-82e3-4a9d5bce9b74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:54,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37542c67-4e5c-4a8e-82e3-4a9d5bce9b74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:54,729] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:54,730] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:54,730] [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 profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	100.0	1512	1512	95	conclusive
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	83.8977	711	1512	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	80.7783	608	1512	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	80.0316	615	1512	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	79.8977	546	1512	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.8774	534	1512	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	79.5247	540	1512	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	79.4312	584	1512	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	79.266	590	1512	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	79.2021	567	1512	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	79.1789	616	1512	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	79.1762	470	1512	95	below_threshold
Sphingomonas montana	strain=W16RD	GCA_001956315.1	1843236	1843236	type	True	78.9817	471	1512	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.9744	489	1512	95	below_threshold
Sphingomonas prati	strain=CGMCC 1.15645	GCA_014643515.1	1843237	1843237	type	True	78.8573	480	1512	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.8497	558	1512	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	78.8096	485	1512	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.6783	426	1512	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	78.6348	409	1512	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	78.3673	457	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:54,732] [INFO] DFAST Taxonomy check result was written to GCF_009739515.1_ASM973951v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:54,732] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:54,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:54,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37542c67-4e5c-4a8e-82e3-4a9d5bce9b74/dqc_reference/checkm_data
[2024-01-25 18:06:54,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:54,789] [INFO] Task started: CheckM
[2024-01-25 18:06:54,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009739515.1_ASM973951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009739515.1_ASM973951v1_genomic.fna/checkm_input GCF_009739515.1_ASM973951v1_genomic.fna/checkm_result
[2024-01-25 18:07:40,446] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:40,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:40,460] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:40,461] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:40,461] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009739515.1_ASM973951v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:40,461] [INFO] Task started: Blastn
[2024-01-25 18:07:40,461] [INFO] Running command: blastn -query GCF_009739515.1_ASM973951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37542c67-4e5c-4a8e-82e3-4a9d5bce9b74/dqc_reference/reference_markers_gtdb.fasta -out GCF_009739515.1_ASM973951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:42,523] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:42,526] [INFO] Selected 22 target genomes.
[2024-01-25 18:07:42,526] [INFO] Target genome list was writen to GCF_009739515.1_ASM973951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:42,541] [INFO] Task started: fastANI
[2024-01-25 18:07:42,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbaca51f-ab3e-4790-baeb-65d5dd34abc9/GCF_009739515.1_ASM973951v1_genomic.fna.gz --refList GCF_009739515.1_ASM973951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009739515.1_ASM973951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:03,876] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:03,890] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:08:03,891] [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_009739515.1	s__Sphingomonas_G sp009739515	100.0	1512	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007785815.1	s__Sphingomonas_G solaris	83.8669	713	1512	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_003034225.1	s__Sphingomonas_E fennica	80.8014	606	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	80.0027	622	1512	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_003050615.1	s__Sphingomonas_H oleivorans	79.9182	530	1512	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_002355275.1	s__Rhizorhabdus dicambivorans	79.8701	549	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.99	99.99	1.00	0.99	3	-
GCF_000016765.1	s__Rhizorhabdus wittichii	79.7282	650	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_018863195.1	s__XMGL2 sp018863195	79.7214	532	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__XMGL2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	79.5525	537	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	79.4687	468	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	79.4356	583	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	79.4245	343	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	79.2194	594	1512	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_001956315.1	s__Sphingomonas_G montana	78.9958	469	1512	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_003345355.1	s__Sphingomonas sp003345355	78.9483	492	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643515.1	s__Sphingomonas_G prati	78.8475	481	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	100.00	100.00	1.00	1.00	3	-
GCF_009913435.1	s__Sphingomonas_B sp009913435	78.6587	427	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107325.1	s__Sphingomonas sp016107325	78.6478	493	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	78.4937	323	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	78.4055	455	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	78.0527	441	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340945.1	s__Sphingomonas sp004340945	77.8688	418	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.25	95.25	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:08:03,893] [INFO] GTDB search result was written to GCF_009739515.1_ASM973951v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:03,894] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:03,899] [INFO] DFAST_QC result json was written to GCF_009739515.1_ASM973951v1_genomic.fna/dqc_result.json
[2024-01-25 18:08:03,899] [INFO] DFAST_QC completed!
[2024-01-25 18:08:03,899] [INFO] Total running time: 0h1m43s