[2024-01-24 15:18:05,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:05,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:05,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg7082983f-348a-4f16-8e0b-e1c0f4574504/dqc_reference
[2024-01-24 15:18:07,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:07,532] [INFO] Task started: Prodigal
[2024-01-24 15:18:07,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cad32dc-fb1a-4a5a-9bdc-a910d70cf9b6/GCF_003201955.1_ASM320195v1_genomic.fna.gz | prodigal -d GCF_003201955.1_ASM320195v1_genomic.fna/cds.fna -a GCF_003201955.1_ASM320195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:19,795] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:19,795] [INFO] Task started: HMMsearch
[2024-01-24 15:18:19,795] [INFO] Running command: hmmsearch --tblout GCF_003201955.1_ASM320195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7082983f-348a-4f16-8e0b-e1c0f4574504/dqc_reference/reference_markers.hmm GCF_003201955.1_ASM320195v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:20,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:20,109] [INFO] Found 6/6 markers.
[2024-01-24 15:18:20,152] [INFO] Query marker FASTA was written to GCF_003201955.1_ASM320195v1_genomic.fna/markers.fasta
[2024-01-24 15:18:20,152] [INFO] Task started: Blastn
[2024-01-24 15:18:20,152] [INFO] Running command: blastn -query GCF_003201955.1_ASM320195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7082983f-348a-4f16-8e0b-e1c0f4574504/dqc_reference/reference_markers.fasta -out GCF_003201955.1_ASM320195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:20,989] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:20,993] [INFO] Selected 25 target genomes.
[2024-01-24 15:18:20,993] [INFO] Target genome list was writen to GCF_003201955.1_ASM320195v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:21,035] [INFO] Task started: fastANI
[2024-01-24 15:18:21,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cad32dc-fb1a-4a5a-9bdc-a910d70cf9b6/GCF_003201955.1_ASM320195v1_genomic.fna.gz --refList GCF_003201955.1_ASM320195v1_genomic.fna/target_genomes.txt --output GCF_003201955.1_ASM320195v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:38,502] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:38,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7082983f-348a-4f16-8e0b-e1c0f4574504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:38,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7082983f-348a-4f16-8e0b-e1c0f4574504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:38,525] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:38,525] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:38,526] [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
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	84.0716	921	1319	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	82.7382	830	1319	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	79.5336	417	1319	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	78.5918	369	1319	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.532	370	1319	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.4701	410	1319	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.3575	399	1319	95	below_threshold
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	78.3343	329	1319	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	78.2951	376	1319	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	78.2277	351	1319	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	78.227	335	1319	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.2226	385	1319	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	78.1377	352	1319	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.0995	333	1319	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	78.0888	339	1319	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	78.0487	310	1319	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.0395	295	1319	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	78.0343	329	1319	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	77.9588	337	1319	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	77.7973	336	1319	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.7903	236	1319	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.7228	336	1319	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.7124	240	1319	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.6849	341	1319	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	77.2806	173	1319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:38,527] [INFO] DFAST Taxonomy check result was written to GCF_003201955.1_ASM320195v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:38,528] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:38,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:38,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7082983f-348a-4f16-8e0b-e1c0f4574504/dqc_reference/checkm_data
[2024-01-24 15:18:38,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:38,570] [INFO] Task started: CheckM
[2024-01-24 15:18:38,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201955.1_ASM320195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201955.1_ASM320195v1_genomic.fna/checkm_input GCF_003201955.1_ASM320195v1_genomic.fna/checkm_result
[2024-01-24 15:19:17,803] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:17,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:17,830] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:17,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:17,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201955.1_ASM320195v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:17,831] [INFO] Task started: Blastn
[2024-01-24 15:19:17,831] [INFO] Running command: blastn -query GCF_003201955.1_ASM320195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7082983f-348a-4f16-8e0b-e1c0f4574504/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201955.1_ASM320195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:19,294] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:19,298] [INFO] Selected 7 target genomes.
[2024-01-24 15:19:19,298] [INFO] Target genome list was writen to GCF_003201955.1_ASM320195v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:19,314] [INFO] Task started: fastANI
[2024-01-24 15:19:19,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cad32dc-fb1a-4a5a-9bdc-a910d70cf9b6/GCF_003201955.1_ASM320195v1_genomic.fna.gz --refList GCF_003201955.1_ASM320195v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201955.1_ASM320195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:26,185] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:26,199] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:26,199] [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_003201955.1	s__Blastomonas natatoria	100.0	1319	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001555775.1	s__Blastomonas delafieldii_A	88.4046	959	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	99.74	98.25	0.90	0.81	22	-
GCF_013607875.1	s__Blastomonas ursincola	88.1155	969	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	97.82	97.14	0.88	0.79	7	-
GCA_000503195.1	s__Blastomonas sp000503195	87.9354	935	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	97.00	97.00	0.84	0.84	2	-
GCF_000786215.1	s__Blastomonas sp000786215	84.8816	947	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331245.1	s__Blastomonas sp000331245	84.4059	910	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003431825.1	s__Blastomonas fulva	84.0697	922	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	98.01	97.97	0.88	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:26,201] [INFO] GTDB search result was written to GCF_003201955.1_ASM320195v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:26,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:26,205] [INFO] DFAST_QC result json was written to GCF_003201955.1_ASM320195v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:26,206] [INFO] DFAST_QC completed!
[2024-01-24 15:19:26,206] [INFO] Total running time: 0h1m21s