[2024-01-24 13:01:23,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:23,042] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:23,042] [INFO] DQC Reference Directory: /var/lib/cwl/stg84d6df8d-de77-47c8-b5e1-2e5c1f4cdd0c/dqc_reference
[2024-01-24 13:01:24,289] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:24,290] [INFO] Task started: Prodigal
[2024-01-24 13:01:24,290] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb2431a7-ac88-404a-ab06-42e05dd7a232/GCF_001598535.1_ASM159853v1_genomic.fna.gz | prodigal -d GCF_001598535.1_ASM159853v1_genomic.fna/cds.fna -a GCF_001598535.1_ASM159853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:36,371] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:36,372] [INFO] Task started: HMMsearch
[2024-01-24 13:01:36,372] [INFO] Running command: hmmsearch --tblout GCF_001598535.1_ASM159853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84d6df8d-de77-47c8-b5e1-2e5c1f4cdd0c/dqc_reference/reference_markers.hmm GCF_001598535.1_ASM159853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:36,687] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:36,689] [INFO] Found 6/6 markers.
[2024-01-24 13:01:36,736] [INFO] Query marker FASTA was written to GCF_001598535.1_ASM159853v1_genomic.fna/markers.fasta
[2024-01-24 13:01:36,737] [INFO] Task started: Blastn
[2024-01-24 13:01:36,737] [INFO] Running command: blastn -query GCF_001598535.1_ASM159853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d6df8d-de77-47c8-b5e1-2e5c1f4cdd0c/dqc_reference/reference_markers.fasta -out GCF_001598535.1_ASM159853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:37,671] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:37,675] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:37,675] [INFO] Target genome list was writen to GCF_001598535.1_ASM159853v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:37,690] [INFO] Task started: fastANI
[2024-01-24 13:01:37,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb2431a7-ac88-404a-ab06-42e05dd7a232/GCF_001598535.1_ASM159853v1_genomic.fna.gz --refList GCF_001598535.1_ASM159853v1_genomic.fna/target_genomes.txt --output GCF_001598535.1_ASM159853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:49,508] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:49,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84d6df8d-de77-47c8-b5e1-2e5c1f4cdd0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:49,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84d6df8d-de77-47c8-b5e1-2e5c1f4cdd0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:49,521] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:01:49,521] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:49,521] [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=NBRC 16415	GCA_001598535.1	76947	76947	type	True	100.0	1314	1323	95	conclusive
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_000632125.2	76947	76947	type	True	99.9934	1296	1323	95	conclusive
Sphingobium herbicidovorans	strain=MH	GCA_002080435.1	76947	76947	type	True	99.9905	1322	1323	95	conclusive
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	83.4013	720	1323	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	83.0716	713	1323	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	82.8908	668	1323	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	82.6695	690	1323	95	below_threshold
Sphingobium vermicomposti	strain=DSM 21299	GCA_011762025.1	529005	529005	type	True	82.4421	703	1323	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	81.6272	600	1323	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	78.3889	305	1323	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.0322	277	1323	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.4341	255	1323	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.3215	265	1323	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.9355	293	1323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:49,523] [INFO] DFAST Taxonomy check result was written to GCF_001598535.1_ASM159853v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:49,523] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:49,523] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:49,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84d6df8d-de77-47c8-b5e1-2e5c1f4cdd0c/dqc_reference/checkm_data
[2024-01-24 13:01:49,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:49,566] [INFO] Task started: CheckM
[2024-01-24 13:01:49,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001598535.1_ASM159853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001598535.1_ASM159853v1_genomic.fna/checkm_input GCF_001598535.1_ASM159853v1_genomic.fna/checkm_result
[2024-01-24 13:02:27,875] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:27,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:27,902] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:27,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:27,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001598535.1_ASM159853v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:27,904] [INFO] Task started: Blastn
[2024-01-24 13:02:27,904] [INFO] Running command: blastn -query GCF_001598535.1_ASM159853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d6df8d-de77-47c8-b5e1-2e5c1f4cdd0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001598535.1_ASM159853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:29,536] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:29,541] [INFO] Selected 13 target genomes.
[2024-01-24 13:02:29,541] [INFO] Target genome list was writen to GCF_001598535.1_ASM159853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:29,568] [INFO] Task started: fastANI
[2024-01-24 13:02:29,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb2431a7-ac88-404a-ab06-42e05dd7a232/GCF_001598535.1_ASM159853v1_genomic.fna.gz --refList GCF_001598535.1_ASM159853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001598535.1_ASM159853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:41,640] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:41,655] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:41,656] [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	99.9905	1322	1323	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	91.9033	902	1323	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	84.4848	847	1323	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	83.577	805	1323	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	83.4454	807	1323	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	83.3924	721	1323	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	83.0716	713	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	82.8502	671	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_001563265.1	s__Sphingobium sp001563265	82.7011	748	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.38	97.84	0.74	0.68	3	-
GCF_008692605.1	s__Sphingobium estronivorans	82.6695	690	1323	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	82.5011	685	1323	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	81.6761	657	1323	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	81.6189	601	1323	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 13:02:41,659] [INFO] GTDB search result was written to GCF_001598535.1_ASM159853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:41,659] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:41,663] [INFO] DFAST_QC result json was written to GCF_001598535.1_ASM159853v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:41,663] [INFO] DFAST_QC completed!
[2024-01-24 13:02:41,663] [INFO] Total running time: 0h1m19s