[2024-01-24 13:58:41,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:41,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:41,049] [INFO] DQC Reference Directory: /var/lib/cwl/stgce86bd9d-bcb9-4928-be49-ef2d641c4b86/dqc_reference
[2024-01-24 13:58:42,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:42,377] [INFO] Task started: Prodigal
[2024-01-24 13:58:42,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg866064cb-05cd-4854-a707-563751727ebd/GCF_013778325.1_ASM1377832v1_genomic.fna.gz | prodigal -d GCF_013778325.1_ASM1377832v1_genomic.fna/cds.fna -a GCF_013778325.1_ASM1377832v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:55,792] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:55,793] [INFO] Task started: HMMsearch
[2024-01-24 13:58:55,793] [INFO] Running command: hmmsearch --tblout GCF_013778325.1_ASM1377832v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce86bd9d-bcb9-4928-be49-ef2d641c4b86/dqc_reference/reference_markers.hmm GCF_013778325.1_ASM1377832v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:56,099] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:56,101] [INFO] Found 6/6 markers.
[2024-01-24 13:58:56,149] [INFO] Query marker FASTA was written to GCF_013778325.1_ASM1377832v1_genomic.fna/markers.fasta
[2024-01-24 13:58:56,149] [INFO] Task started: Blastn
[2024-01-24 13:58:56,149] [INFO] Running command: blastn -query GCF_013778325.1_ASM1377832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce86bd9d-bcb9-4928-be49-ef2d641c4b86/dqc_reference/reference_markers.fasta -out GCF_013778325.1_ASM1377832v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:57,221] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:57,225] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:57,225] [INFO] Target genome list was writen to GCF_013778325.1_ASM1377832v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:57,236] [INFO] Task started: fastANI
[2024-01-24 13:58:57,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg866064cb-05cd-4854-a707-563751727ebd/GCF_013778325.1_ASM1377832v1_genomic.fna.gz --refList GCF_013778325.1_ASM1377832v1_genomic.fna/target_genomes.txt --output GCF_013778325.1_ASM1377832v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:13,394] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:13,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce86bd9d-bcb9-4928-be49-ef2d641c4b86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:13,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce86bd9d-bcb9-4928-be49-ef2d641c4b86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:13,407] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:13,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:13,408] [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 chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	100.0	1443	1444	95	conclusive
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	82.9894	703	1444	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	80.6349	587	1444	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.7121	488	1444	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	79.599	545	1444	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	79.4752	501	1444	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	79.402	515	1444	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	79.1624	445	1444	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	79.1399	505	1444	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	79.0859	544	1444	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.0523	477	1444	95	below_threshold
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	78.9703	426	1444	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	78.9461	525	1444	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.7543	376	1444	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.6241	398	1444	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.5356	453	1444	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	77.4849	293	1444	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:13,409] [INFO] DFAST Taxonomy check result was written to GCF_013778325.1_ASM1377832v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:13,410] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:13,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:13,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce86bd9d-bcb9-4928-be49-ef2d641c4b86/dqc_reference/checkm_data
[2024-01-24 13:59:13,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:13,452] [INFO] Task started: CheckM
[2024-01-24 13:59:13,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013778325.1_ASM1377832v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013778325.1_ASM1377832v1_genomic.fna/checkm_input GCF_013778325.1_ASM1377832v1_genomic.fna/checkm_result
[2024-01-24 13:59:53,609] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:53,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:53,630] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:53,630] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:53,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013778325.1_ASM1377832v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:53,631] [INFO] Task started: Blastn
[2024-01-24 13:59:53,631] [INFO] Running command: blastn -query GCF_013778325.1_ASM1377832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce86bd9d-bcb9-4928-be49-ef2d641c4b86/dqc_reference/reference_markers_gtdb.fasta -out GCF_013778325.1_ASM1377832v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:55,450] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:55,454] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:55,455] [INFO] Target genome list was writen to GCF_013778325.1_ASM1377832v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:55,465] [INFO] Task started: fastANI
[2024-01-24 13:59:55,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg866064cb-05cd-4854-a707-563751727ebd/GCF_013778325.1_ASM1377832v1_genomic.fna.gz --refList GCF_013778325.1_ASM1377832v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013778325.1_ASM1377832v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:04,648] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:04,665] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:04,665] [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_013778325.1	s__Sphingomonas_N chungangi	100.0	1443	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_000333335.1	s__Sphingomonas_N sp000333335	87.1142	648	1444	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_000383095.1	s__Sphingomonas_N sp000383095	83.1527	682	1444	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_011762195.1	s__Sphingomonas_N oligoaromativorans	82.9891	703	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871605.1	s__Sphingomonas_N sp903871605	82.0231	703	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000016765.1	s__Rhizorhabdus wittichii	79.7808	552	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_013113735.1	s__Sphingomonas_I sp013113735	79.4221	519	1444	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_903644055.1	s__Sphingomonas_I sp903644055	79.3522	338	1444	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	78.956	525	1444	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_014396585.1	s__Sphingomicrobium rhizophilum	77.9866	270	1444	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:04,667] [INFO] GTDB search result was written to GCF_013778325.1_ASM1377832v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:04,667] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:04,671] [INFO] DFAST_QC result json was written to GCF_013778325.1_ASM1377832v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:04,671] [INFO] DFAST_QC completed!
[2024-01-24 14:00:04,671] [INFO] Total running time: 0h1m24s