[2024-01-25 20:12:05,488] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg743b3056-3375-440e-b837-25600d71a38d/dqc_reference
[2024-01-25 20:12:06,617] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:06,617] [INFO] Task started: Prodigal
[2024-01-25 20:12:06,618] [INFO] Running command: gunzip -c /var/lib/cwl/stgd60672d2-b1af-4e22-b454-113af282625d/GCF_011926545.1_ASM1192654v1_genomic.fna.gz | prodigal -d GCF_011926545.1_ASM1192654v1_genomic.fna/cds.fna -a GCF_011926545.1_ASM1192654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:16,696] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:16,697] [INFO] Task started: HMMsearch
[2024-01-25 20:12:16,697] [INFO] Running command: hmmsearch --tblout GCF_011926545.1_ASM1192654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg743b3056-3375-440e-b837-25600d71a38d/dqc_reference/reference_markers.hmm GCF_011926545.1_ASM1192654v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:16,914] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:16,915] [INFO] Found 6/6 markers.
[2024-01-25 20:12:16,950] [INFO] Query marker FASTA was written to GCF_011926545.1_ASM1192654v1_genomic.fna/markers.fasta
[2024-01-25 20:12:16,951] [INFO] Task started: Blastn
[2024-01-25 20:12:16,951] [INFO] Running command: blastn -query GCF_011926545.1_ASM1192654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg743b3056-3375-440e-b837-25600d71a38d/dqc_reference/reference_markers.fasta -out GCF_011926545.1_ASM1192654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:17,815] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:17,817] [INFO] Selected 19 target genomes.
[2024-01-25 20:12:17,818] [INFO] Target genome list was writen to GCF_011926545.1_ASM1192654v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:17,830] [INFO] Task started: fastANI
[2024-01-25 20:12:17,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgd60672d2-b1af-4e22-b454-113af282625d/GCF_011926545.1_ASM1192654v1_genomic.fna.gz --refList GCF_011926545.1_ASM1192654v1_genomic.fna/target_genomes.txt --output GCF_011926545.1_ASM1192654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:34,638] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:34,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg743b3056-3375-440e-b837-25600d71a38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:34,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg743b3056-3375-440e-b837-25600d71a38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:34,654] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:34,654] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:34,654] [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
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	100.0	1343	1343	95	conclusive
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	87.1597	1022	1343	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	86.1803	953	1343	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	85.9239	844	1343	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	85.5012	840	1343	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	85.4733	877	1343	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	85.4308	809	1343	95	below_threshold
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	84.7509	866	1343	95	below_threshold
Sphingopyxis bauzanensis	strain=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	84.7482	867	1343	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	84.546	821	1343	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	84.4352	737	1343	95	below_threshold
Sphingopyxis witflariensis	strain=DSM 14551	GCA_002205635.1	173675	173675	type	True	84.1738	864	1343	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	84.0264	804	1343	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	83.9589	804	1343	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.391	447	1343	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	78.1325	397	1343	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.927	375	1343	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.8185	399	1343	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.6719	421	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:34,657] [INFO] DFAST Taxonomy check result was written to GCF_011926545.1_ASM1192654v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:34,659] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:34,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:34,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg743b3056-3375-440e-b837-25600d71a38d/dqc_reference/checkm_data
[2024-01-25 20:12:34,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:34,701] [INFO] Task started: CheckM
[2024-01-25 20:12:34,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011926545.1_ASM1192654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011926545.1_ASM1192654v1_genomic.fna/checkm_input GCF_011926545.1_ASM1192654v1_genomic.fna/checkm_result
[2024-01-25 20:13:05,741] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:05,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:05,775] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:05,776] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:05,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011926545.1_ASM1192654v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:05,776] [INFO] Task started: Blastn
[2024-01-25 20:13:05,776] [INFO] Running command: blastn -query GCF_011926545.1_ASM1192654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg743b3056-3375-440e-b837-25600d71a38d/dqc_reference/reference_markers_gtdb.fasta -out GCF_011926545.1_ASM1192654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:07,542] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:07,545] [INFO] Selected 13 target genomes.
[2024-01-25 20:13:07,545] [INFO] Target genome list was writen to GCF_011926545.1_ASM1192654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:07,567] [INFO] Task started: fastANI
[2024-01-25 20:13:07,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgd60672d2-b1af-4e22-b454-113af282625d/GCF_011926545.1_ASM1192654v1_genomic.fna.gz --refList GCF_011926545.1_ASM1192654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011926545.1_ASM1192654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:22,031] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:22,040] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:22,041] [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_011926545.1	s__Sphingopyxis italica	100.0	1343	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000756385.1	s__Sphingopyxis sp000756385	90.6611	1113	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	90.5123	1060	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795895.1	s__Sphingopyxis sp004795895	89.6905	1089	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410105.1	s__Sphingopyxis sp013410105	88.8906	1039	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCF_001468225.1	s__Sphingopyxis sp001468225	88.547	1072	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.97	0.98	0.96	8	-
GCA_005503215.1	s__Sphingopyxis sp005503215	87.7944	1016	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.20	99.20	0.88	0.88	2	-
GCF_000756375.1	s__Sphingopyxis sp000756375	87.6816	1009	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463645.1	s__Sphingopyxis sp016463645	87.6625	887	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427105.1	s__Sphingopyxis sp001427105	87.2688	990	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000803645.1	s__Sphingopyxis fribergensis	87.1709	1022	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745175.1	s__Sphingopyxis sp017745175	87.1509	878	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873485.1	s__Sphingopyxis sp014873485	87.0432	1022	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:22,042] [INFO] GTDB search result was written to GCF_011926545.1_ASM1192654v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:22,043] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:22,046] [INFO] DFAST_QC result json was written to GCF_011926545.1_ASM1192654v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:22,046] [INFO] DFAST_QC completed!
[2024-01-25 20:13:22,046] [INFO] Total running time: 0h1m17s