[2024-01-25 19:02:35,636] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:35,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:35,638] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbd08a3b-1e75-49d4-b247-c18453a01d55/dqc_reference
[2024-01-25 19:02:36,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:36,807] [INFO] Task started: Prodigal
[2024-01-25 19:02:36,807] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5f5c1a5-bb66-4a78-b2c1-eaeb264870b0/GCF_026157185.1_ASM2615718v1_genomic.fna.gz | prodigal -d GCF_026157185.1_ASM2615718v1_genomic.fna/cds.fna -a GCF_026157185.1_ASM2615718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:42,380] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:42,381] [INFO] Task started: HMMsearch
[2024-01-25 19:02:42,381] [INFO] Running command: hmmsearch --tblout GCF_026157185.1_ASM2615718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbd08a3b-1e75-49d4-b247-c18453a01d55/dqc_reference/reference_markers.hmm GCF_026157185.1_ASM2615718v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:42,583] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:42,584] [INFO] Found 6/6 markers.
[2024-01-25 19:02:42,606] [INFO] Query marker FASTA was written to GCF_026157185.1_ASM2615718v1_genomic.fna/markers.fasta
[2024-01-25 19:02:42,606] [INFO] Task started: Blastn
[2024-01-25 19:02:42,606] [INFO] Running command: blastn -query GCF_026157185.1_ASM2615718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbd08a3b-1e75-49d4-b247-c18453a01d55/dqc_reference/reference_markers.fasta -out GCF_026157185.1_ASM2615718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:43,469] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:43,472] [INFO] Selected 13 target genomes.
[2024-01-25 19:02:43,472] [INFO] Target genome list was writen to GCF_026157185.1_ASM2615718v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:43,482] [INFO] Task started: fastANI
[2024-01-25 19:02:43,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5f5c1a5-bb66-4a78-b2c1-eaeb264870b0/GCF_026157185.1_ASM2615718v1_genomic.fna.gz --refList GCF_026157185.1_ASM2615718v1_genomic.fna/target_genomes.txt --output GCF_026157185.1_ASM2615718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:51,333] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:51,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbd08a3b-1e75-49d4-b247-c18453a01d55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:51,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbd08a3b-1e75-49d4-b247-c18453a01d55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:51,343] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:51,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:51,344] [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
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	99.9984	692	692	95	conclusive
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	80.7136	503	692	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	80.1507	433	692	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	80.1079	451	692	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	79.9983	435	692	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	78.4465	305	692	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.0054	244	692	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	77.999	268	692	95	below_threshold
Sphingorhabdus soli	strain=D-2Q-5-6	GCA_007995095.1	2601267	2601267	type	True	77.8351	227	692	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.764	262	692	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	77.6398	248	692	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.3415	185	692	95	below_threshold
Sphingomonas guangdongensis	strain=CGMCC 1.12672	GCA_900199185.1	1141890	1141890	type	True	77.0106	154	692	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:51,345] [INFO] DFAST Taxonomy check result was written to GCF_026157185.1_ASM2615718v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:51,346] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:51,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:51,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbd08a3b-1e75-49d4-b247-c18453a01d55/dqc_reference/checkm_data
[2024-01-25 19:02:51,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:51,370] [INFO] Task started: CheckM
[2024-01-25 19:02:51,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026157185.1_ASM2615718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026157185.1_ASM2615718v1_genomic.fna/checkm_input GCF_026157185.1_ASM2615718v1_genomic.fna/checkm_result
[2024-01-25 19:03:12,243] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:12,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:12,261] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:12,261] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:12,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026157185.1_ASM2615718v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:12,262] [INFO] Task started: Blastn
[2024-01-25 19:03:12,262] [INFO] Running command: blastn -query GCF_026157185.1_ASM2615718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbd08a3b-1e75-49d4-b247-c18453a01d55/dqc_reference/reference_markers_gtdb.fasta -out GCF_026157185.1_ASM2615718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:13,972] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:13,975] [INFO] Selected 20 target genomes.
[2024-01-25 19:03:13,975] [INFO] Target genome list was writen to GCF_026157185.1_ASM2615718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:13,990] [INFO] Task started: fastANI
[2024-01-25 19:03:13,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5f5c1a5-bb66-4a78-b2c1-eaeb264870b0/GCF_026157185.1_ASM2615718v1_genomic.fna.gz --refList GCF_026157185.1_ASM2615718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026157185.1_ASM2615718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:25,341] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:25,353] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:25,354] [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_014195685.1	s__Sphingomicrobium lutaoense	99.9984	692	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013001055.1	s__Sphingomicrobium sp004282935	79.0508	342	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	99.85	99.85	0.95	0.95	2	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	78.7708	332	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711715.1	s__Sphingomicrobium astaxanthinifaciens	78.5209	320	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396585.1	s__Sphingomicrobium rhizophilum	78.5062	279	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003499275.1	s__Sphingomicrobium mesophila	78.4335	306	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	78.3596	275	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	78.0764	238	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007998985.1	s__Sphingomicrobium xanthus	77.9992	268	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	77.8844	266	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011301715.1	s__Sphingomicrobium sp011301715	77.8248	216	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583725.1	s__Sphingomicrobium edaphi	77.7373	209	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	77.6653	246	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242355.1	s__Sphingomicrobium sp019242355	77.6086	178	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355855.1	s__Sphingobium cloacae	77.5783	198	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019247755.1	s__Sphingomicrobium sp019247755	77.438	149	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	77.3574	158	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012035195.1	s__Sphingomonas sp012035195	77.3264	186	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	77.2836	197	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745295.1	s__Novosphingobium sp017745295	76.8265	155	692	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:25,356] [INFO] GTDB search result was written to GCF_026157185.1_ASM2615718v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:25,357] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:25,360] [INFO] DFAST_QC result json was written to GCF_026157185.1_ASM2615718v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:25,360] [INFO] DFAST_QC completed!
[2024-01-25 19:03:25,361] [INFO] Total running time: 0h0m50s