[2024-01-24 11:35:11,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,972] [INFO] DQC Reference Directory: /var/lib/cwl/stgaafb12e0-df3a-46e1-8532-26fdcd52be94/dqc_reference
[2024-01-24 11:35:14,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:14,416] [INFO] Task started: Prodigal
[2024-01-24 11:35:14,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg17d9e2b9-fe6b-4b4a-a102-c9197c47ed63/GCF_014199405.1_ASM1419940v1_genomic.fna.gz | prodigal -d GCF_014199405.1_ASM1419940v1_genomic.fna/cds.fna -a GCF_014199405.1_ASM1419940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:25,392] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:25,392] [INFO] Task started: HMMsearch
[2024-01-24 11:35:25,392] [INFO] Running command: hmmsearch --tblout GCF_014199405.1_ASM1419940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaafb12e0-df3a-46e1-8532-26fdcd52be94/dqc_reference/reference_markers.hmm GCF_014199405.1_ASM1419940v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:25,670] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:25,671] [INFO] Found 6/6 markers.
[2024-01-24 11:35:25,703] [INFO] Query marker FASTA was written to GCF_014199405.1_ASM1419940v1_genomic.fna/markers.fasta
[2024-01-24 11:35:25,703] [INFO] Task started: Blastn
[2024-01-24 11:35:25,703] [INFO] Running command: blastn -query GCF_014199405.1_ASM1419940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaafb12e0-df3a-46e1-8532-26fdcd52be94/dqc_reference/reference_markers.fasta -out GCF_014199405.1_ASM1419940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:26,765] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:26,768] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:26,768] [INFO] Target genome list was writen to GCF_014199405.1_ASM1419940v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:26,774] [INFO] Task started: fastANI
[2024-01-24 11:35:26,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg17d9e2b9-fe6b-4b4a-a102-c9197c47ed63/GCF_014199405.1_ASM1419940v1_genomic.fna.gz --refList GCF_014199405.1_ASM1419940v1_genomic.fna/target_genomes.txt --output GCF_014199405.1_ASM1419940v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:37,929] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:37,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaafb12e0-df3a-46e1-8532-26fdcd52be94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:37,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaafb12e0-df3a-46e1-8532-26fdcd52be94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:37,941] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:35:37,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:37,942] [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 prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	100.0	1255	1255	95	conclusive
Sphingomonas prati	strain=CGMCC 1.15645	GCA_014643515.1	1843237	1843237	type	True	99.9977	1253	1255	95	conclusive
Sphingomonas prati	strain=W18RD	GCA_009755805.1	1843237	1843237	type	True	99.9976	1250	1255	95	conclusive
Sphingomonas montana	strain=W16RD	GCA_001956315.1	1843236	1843236	type	True	86.7651	793	1255	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	79.2642	438	1255	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.8942	476	1255	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	78.296	432	1255	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.2227	333	1255	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	78.085	341	1255	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.9421	452	1255	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.9395	457	1255	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.9201	472	1255	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.7159	308	1255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:37,943] [INFO] DFAST Taxonomy check result was written to GCF_014199405.1_ASM1419940v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:37,944] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:37,944] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:37,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaafb12e0-df3a-46e1-8532-26fdcd52be94/dqc_reference/checkm_data
[2024-01-24 11:35:37,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:37,983] [INFO] Task started: CheckM
[2024-01-24 11:35:37,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199405.1_ASM1419940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199405.1_ASM1419940v1_genomic.fna/checkm_input GCF_014199405.1_ASM1419940v1_genomic.fna/checkm_result
[2024-01-24 11:36:13,033] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:13,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:13,053] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:13,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:13,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199405.1_ASM1419940v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:13,054] [INFO] Task started: Blastn
[2024-01-24 11:36:13,055] [INFO] Running command: blastn -query GCF_014199405.1_ASM1419940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaafb12e0-df3a-46e1-8532-26fdcd52be94/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199405.1_ASM1419940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:15,104] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:15,108] [INFO] Selected 17 target genomes.
[2024-01-24 11:36:15,108] [INFO] Target genome list was writen to GCF_014199405.1_ASM1419940v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:15,122] [INFO] Task started: fastANI
[2024-01-24 11:36:15,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg17d9e2b9-fe6b-4b4a-a102-c9197c47ed63/GCF_014199405.1_ASM1419940v1_genomic.fna.gz --refList GCF_014199405.1_ASM1419940v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199405.1_ASM1419940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:28,203] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:28,220] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:28,220] [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_014643515.1	s__Sphingomonas_G prati	99.9977	1253	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_001956315.1	s__Sphingomonas_G montana	86.8044	791	1255	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_007785815.1	s__Sphingomonas_G solaris	79.2496	439	1255	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_009739515.1	s__Sphingomonas_G sp009739515	78.8953	476	1255	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_018139225.1	s__Sphingomonas sp018139225	78.6704	425	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001429065.1	s__Rhizorhabdus sp001429065	78.6652	354	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762195.1	s__Sphingomonas_N oligoaromativorans	78.5527	399	1255	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_001428605.1	s__Rhizorhabdus sp001428605	78.5372	418	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001421505.1	s__Sphingomonas sp001421505	78.4825	427	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	78.4746	423	1255	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_001421765.1	s__Sphingomonas sp001421765	78.3511	427	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_011044255.1	s__Rhizorhabdus sp011044255	78.1206	337	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	78.0914	307	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721295.1	s__Sphingomonas turrisvirgatae	78.0659	301	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753715.1	s__Sphingomonas_B horti	78.06	364	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001421995.1	s__Sphingomonas sp001421995	77.9218	378	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995055.1	s__Allosphingosinicella ginsenosidimutans	77.6527	314	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:28,223] [INFO] GTDB search result was written to GCF_014199405.1_ASM1419940v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:28,223] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:28,227] [INFO] DFAST_QC result json was written to GCF_014199405.1_ASM1419940v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:28,227] [INFO] DFAST_QC completed!
[2024-01-24 11:36:28,227] [INFO] Total running time: 0h1m16s