[2024-01-24 13:36:45,212] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e0a42d9-cd94-4fb3-88fb-0b520f38c3f3/dqc_reference
[2024-01-24 13:36:46,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,576] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg388662e7-b4e2-4ac0-a592-fcfa7fcb4739/GCF_014199435.1_ASM1419943v1_genomic.fna.gz | prodigal -d GCF_014199435.1_ASM1419943v1_genomic.fna/cds.fna -a GCF_014199435.1_ASM1419943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:58,229] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:58,230] [INFO] Task started: HMMsearch
[2024-01-24 13:36:58,230] [INFO] Running command: hmmsearch --tblout GCF_014199435.1_ASM1419943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e0a42d9-cd94-4fb3-88fb-0b520f38c3f3/dqc_reference/reference_markers.hmm GCF_014199435.1_ASM1419943v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:58,596] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:58,598] [INFO] Found 6/6 markers.
[2024-01-24 13:36:58,632] [INFO] Query marker FASTA was written to GCF_014199435.1_ASM1419943v1_genomic.fna/markers.fasta
[2024-01-24 13:36:58,632] [INFO] Task started: Blastn
[2024-01-24 13:36:58,633] [INFO] Running command: blastn -query GCF_014199435.1_ASM1419943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e0a42d9-cd94-4fb3-88fb-0b520f38c3f3/dqc_reference/reference_markers.fasta -out GCF_014199435.1_ASM1419943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:59,631] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:59,635] [INFO] Selected 23 target genomes.
[2024-01-24 13:36:59,636] [INFO] Target genome list was writen to GCF_014199435.1_ASM1419943v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:59,647] [INFO] Task started: fastANI
[2024-01-24 13:36:59,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg388662e7-b4e2-4ac0-a592-fcfa7fcb4739/GCF_014199435.1_ASM1419943v1_genomic.fna.gz --refList GCF_014199435.1_ASM1419943v1_genomic.fna/target_genomes.txt --output GCF_014199435.1_ASM1419943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:20,159] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:20,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e0a42d9-cd94-4fb3-88fb-0b520f38c3f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:20,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e0a42d9-cd94-4fb3-88fb-0b520f38c3f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:20,177] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:20,178] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:20,178] [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 subterraneum	strain=DSM 102255	GCA_014199435.1	627688	627688	type	True	100.0	1230	1232	95	conclusive
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	80.4555	381	1232	95	below_threshold
Sphingobium wenxiniae	strain=CGMCC 1.7748	GCA_007830065.1	595605	595605	type	True	80.4162	383	1232	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	80.2366	478	1232	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	79.4706	414	1232	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	79.4577	362	1232	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	79.4494	389	1232	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	79.3988	341	1232	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	79.2221	413	1232	95	below_threshold
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	79.1885	371	1232	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	79.0797	371	1232	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	79.0707	360	1232	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	79.0589	369	1232	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	79.0285	377	1232	95	below_threshold
Sphingobium bisphenolivorans	strain=YL23	GCA_000412635.1	1335760	1335760	type	True	78.7899	341	1232	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	78.7742	407	1232	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	78.6956	336	1232	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.2508	274	1232	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.2339	248	1232	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.1824	275	1232	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.8862	205	1232	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.8406	253	1232	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	77.3124	144	1232	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:20,183] [INFO] DFAST Taxonomy check result was written to GCF_014199435.1_ASM1419943v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:20,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:20,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:20,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e0a42d9-cd94-4fb3-88fb-0b520f38c3f3/dqc_reference/checkm_data
[2024-01-24 13:37:20,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:20,227] [INFO] Task started: CheckM
[2024-01-24 13:37:20,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199435.1_ASM1419943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199435.1_ASM1419943v1_genomic.fna/checkm_input GCF_014199435.1_ASM1419943v1_genomic.fna/checkm_result
[2024-01-24 13:37:59,562] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:59,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:59,583] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:59,584] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:59,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199435.1_ASM1419943v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:59,585] [INFO] Task started: Blastn
[2024-01-24 13:37:59,585] [INFO] Running command: blastn -query GCF_014199435.1_ASM1419943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e0a42d9-cd94-4fb3-88fb-0b520f38c3f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199435.1_ASM1419943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:01,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:01,280] [INFO] Selected 23 target genomes.
[2024-01-24 13:38:01,280] [INFO] Target genome list was writen to GCF_014199435.1_ASM1419943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:01,307] [INFO] Task started: fastANI
[2024-01-24 13:38:01,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg388662e7-b4e2-4ac0-a592-fcfa7fcb4739/GCF_014199435.1_ASM1419943v1_genomic.fna.gz --refList GCF_014199435.1_ASM1419943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199435.1_ASM1419943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:19,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:19,257] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:19,258] [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_014199435.1	s__Sphingobium subterraneum	100.0	1230	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014196495.1	s__Sphingobium jiangsuense	80.2123	480	1232	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	79.898	404	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556865.1	s__Sphingobium sp001556865	79.4827	385	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445065.1	s__Sphingobium quisquiliarum	79.3161	344	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	-
GCF_000315525.1	s__Sphingobium yanoikuyae	79.2296	411	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCA_003248935.1	s__Sphingobium sp003248935	79.1791	351	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196635.1	s__Sphingobium fontiphilum	79.1631	374	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375555.1	s__Sphingobium sp013375555	79.0785	383	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393185.1	s__Sphingobium lactosutens_A	79.0136	391	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713415.1	s__Sphingobium sp001713415	78.9016	387	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	95.59	95.59	0.75	0.75	2	-
GCF_014873695.1	s__Sphingobium sp014873695	78.8766	376	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375535.1	s__Sphingobium sp013375535	78.8763	420	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445105.1	s__Sphingobium lactosutens	78.8711	383	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCA_006226685.1	s__Sphingobium sp006226685	78.781	349	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.90	99.90	0.86	0.86	2	-
GCF_000412635.1	s__Sphingobium bisphenolivorans	78.7774	342	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197035.1	s__Sphingobium scionense	78.7709	406	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153545.1	s__Sphingobium sp000153545	78.7471	332	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.72	97.49	0.82	0.71	9	-
GCF_001598335.1	s__Sphingobium abikonense	78.6303	354	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_900218065.1	s__Sphingobium sp900218065	78.5787	317	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.42	97.40	0.85	0.85	5	-
GCF_900109095.1	s__Sphingobium sp900109095	78.5587	388	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002312805.1	s__Sphingobium sp002312805	78.5005	388	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	95.45	95.45	0.84	0.84	2	-
GCF_002855555.1	s__Novosphingobium sp002855555	77.8741	209	1232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:19,260] [INFO] GTDB search result was written to GCF_014199435.1_ASM1419943v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:19,260] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:19,265] [INFO] DFAST_QC result json was written to GCF_014199435.1_ASM1419943v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:19,265] [INFO] DFAST_QC completed!
[2024-01-24 13:38:19,265] [INFO] Total running time: 0h1m34s