[2024-01-24 14:54:56,705] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cf87e69-3cbe-44cd-ae9d-149e43f57ad1/dqc_reference
[2024-01-24 14:54:58,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:58,051] [INFO] Task started: Prodigal
[2024-01-24 14:54:58,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f72613a-2bae-49b4-ac48-e6b8e3790358/GCF_002080435.1_ASM208043v1_genomic.fna.gz | prodigal -d GCF_002080435.1_ASM208043v1_genomic.fna/cds.fna -a GCF_002080435.1_ASM208043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:11,664] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:11,665] [INFO] Task started: HMMsearch
[2024-01-24 14:55:11,665] [INFO] Running command: hmmsearch --tblout GCF_002080435.1_ASM208043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cf87e69-3cbe-44cd-ae9d-149e43f57ad1/dqc_reference/reference_markers.hmm GCF_002080435.1_ASM208043v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:11,962] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:11,963] [INFO] Found 6/6 markers.
[2024-01-24 14:55:12,006] [INFO] Query marker FASTA was written to GCF_002080435.1_ASM208043v1_genomic.fna/markers.fasta
[2024-01-24 14:55:12,006] [INFO] Task started: Blastn
[2024-01-24 14:55:12,006] [INFO] Running command: blastn -query GCF_002080435.1_ASM208043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf87e69-3cbe-44cd-ae9d-149e43f57ad1/dqc_reference/reference_markers.fasta -out GCF_002080435.1_ASM208043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:12,852] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:12,855] [INFO] Selected 14 target genomes.
[2024-01-24 14:55:12,855] [INFO] Target genome list was writen to GCF_002080435.1_ASM208043v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:12,861] [INFO] Task started: fastANI
[2024-01-24 14:55:12,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f72613a-2bae-49b4-ac48-e6b8e3790358/GCF_002080435.1_ASM208043v1_genomic.fna.gz --refList GCF_002080435.1_ASM208043v1_genomic.fna/target_genomes.txt --output GCF_002080435.1_ASM208043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:25,257] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:25,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cf87e69-3cbe-44cd-ae9d-149e43f57ad1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:25,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cf87e69-3cbe-44cd-ae9d-149e43f57ad1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:25,271] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:55:25,271] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:25,272] [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
Sphingobium herbicidovorans	strain=MH	GCA_002080435.1	76947	76947	type	True	100.0	1398	1412	95	conclusive
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_000632125.2	76947	76947	type	True	99.963	1314	1412	95	conclusive
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_001598535.1	76947	76947	type	True	99.9532	1316	1412	95	conclusive
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	83.4523	737	1412	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	83.1752	716	1412	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	82.9509	683	1412	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	82.7684	705	1412	95	below_threshold
Sphingobium vermicomposti	strain=DSM 21299	GCA_011762025.1	529005	529005	type	True	82.3474	724	1412	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	81.8374	618	1412	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	78.496	301	1412	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.2227	291	1412	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.6878	246	1412	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.6768	254	1412	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.2253	290	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:25,273] [INFO] DFAST Taxonomy check result was written to GCF_002080435.1_ASM208043v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:25,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:25,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:25,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cf87e69-3cbe-44cd-ae9d-149e43f57ad1/dqc_reference/checkm_data
[2024-01-24 14:55:25,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:25,319] [INFO] Task started: CheckM
[2024-01-24 14:55:25,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002080435.1_ASM208043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002080435.1_ASM208043v1_genomic.fna/checkm_input GCF_002080435.1_ASM208043v1_genomic.fna/checkm_result
[2024-01-24 14:56:06,605] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:06,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:06,629] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:06,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:06,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002080435.1_ASM208043v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:06,630] [INFO] Task started: Blastn
[2024-01-24 14:56:06,630] [INFO] Running command: blastn -query GCF_002080435.1_ASM208043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf87e69-3cbe-44cd-ae9d-149e43f57ad1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002080435.1_ASM208043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:08,282] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:08,285] [INFO] Selected 13 target genomes.
[2024-01-24 14:56:08,285] [INFO] Target genome list was writen to GCF_002080435.1_ASM208043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:08,299] [INFO] Task started: fastANI
[2024-01-24 14:56:08,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f72613a-2bae-49b4-ac48-e6b8e3790358/GCF_002080435.1_ASM208043v1_genomic.fna.gz --refList GCF_002080435.1_ASM208043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002080435.1_ASM208043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:21,312] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:21,324] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:21,324] [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_002080435.1	s__Sphingobium herbicidovorans	100.0	1401	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_001563285.1	s__Sphingobium sp001563285	91.9389	906	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001658005.1	s__Sphingobium sp001658005	84.5838	861	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900218065.1	s__Sphingobium sp900218065	83.684	789	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.42	97.40	0.85	0.85	5	-
GCF_015693305.1	s__Sphingobium sp015693305	83.5366	808	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005725.1	s__Sphingobium chungbukense	83.4555	737	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_000445065.1	s__Sphingobium quisquiliarum	83.1712	712	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	-
GCF_001563265.1	s__Sphingobium sp001563265	83.0466	752	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.38	97.84	0.74	0.68	3	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	82.9673	682	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_008692605.1	s__Sphingobium estronivorans	82.7721	704	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375535.1	s__Sphingobium sp013375535	82.3709	716	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361945.1	s__Sphingobium barthaii_A	81.9433	653	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447205.1	s__Sphingobium ummariense	81.8399	621	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:21,326] [INFO] GTDB search result was written to GCF_002080435.1_ASM208043v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:21,327] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:21,332] [INFO] DFAST_QC result json was written to GCF_002080435.1_ASM208043v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:21,332] [INFO] DFAST_QC completed!
[2024-01-24 14:56:21,332] [INFO] Total running time: 0h1m25s