[2024-01-24 14:05:53,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9a4ed96-110f-43a4-97ac-e4eba6e66b87/dqc_reference
[2024-01-24 14:05:55,078] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,079] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,079] [INFO] Running command: gunzip -c /var/lib/cwl/stg4854d8e9-3710-444f-8394-86303faf164e/GCF_004005905.1_ASM400590v1_genomic.fna.gz | prodigal -d GCF_004005905.1_ASM400590v1_genomic.fna/cds.fna -a GCF_004005905.1_ASM400590v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:09,555] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:09,555] [INFO] Task started: HMMsearch
[2024-01-24 14:06:09,555] [INFO] Running command: hmmsearch --tblout GCF_004005905.1_ASM400590v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9a4ed96-110f-43a4-97ac-e4eba6e66b87/dqc_reference/reference_markers.hmm GCF_004005905.1_ASM400590v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:09,865] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:09,866] [INFO] Found 6/6 markers.
[2024-01-24 14:06:09,905] [INFO] Query marker FASTA was written to GCF_004005905.1_ASM400590v1_genomic.fna/markers.fasta
[2024-01-24 14:06:09,905] [INFO] Task started: Blastn
[2024-01-24 14:06:09,905] [INFO] Running command: blastn -query GCF_004005905.1_ASM400590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9a4ed96-110f-43a4-97ac-e4eba6e66b87/dqc_reference/reference_markers.fasta -out GCF_004005905.1_ASM400590v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:10,707] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:10,711] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:10,711] [INFO] Target genome list was writen to GCF_004005905.1_ASM400590v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:10,720] [INFO] Task started: fastANI
[2024-01-24 14:06:10,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg4854d8e9-3710-444f-8394-86303faf164e/GCF_004005905.1_ASM400590v1_genomic.fna.gz --refList GCF_004005905.1_ASM400590v1_genomic.fna/target_genomes.txt --output GCF_004005905.1_ASM400590v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:21,941] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:21,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9a4ed96-110f-43a4-97ac-e4eba6e66b87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:21,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9a4ed96-110f-43a4-97ac-e4eba6e66b87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:21,957] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:21,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:21,957] [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
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	100.0	1332	1335	95	conclusive
Novosphingobium sediminicola	strain=DSM 27057	GCA_014196525.1	563162	563162	type	True	81.9299	868	1335	95	below_threshold
Novosphingobium ovatum	strain=FSY-8	GCA_009909235.1	1908523	1908523	type	True	81.3483	687	1335	95	below_threshold
Novosphingobium rosa	strain=NBRC 15208	GCA_001598555.1	76978	76978	type	True	79.7181	597	1335	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.4009	357	1335	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.1427	342	1335	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	78.004	312	1335	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.9655	285	1335	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	77.9374	351	1335	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	77.591	315	1335	95	below_threshold
Novosphingobium fluoreni	strain=DSM 27568	GCA_014196615.1	1391222	1391222	type	True	77.5534	240	1335	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.5236	158	1335	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	77.3254	217	1335	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.2784	154	1335	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:21,959] [INFO] DFAST Taxonomy check result was written to GCF_004005905.1_ASM400590v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:21,959] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:21,960] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:21,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9a4ed96-110f-43a4-97ac-e4eba6e66b87/dqc_reference/checkm_data
[2024-01-24 14:06:21,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:22,002] [INFO] Task started: CheckM
[2024-01-24 14:06:22,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005905.1_ASM400590v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005905.1_ASM400590v1_genomic.fna/checkm_input GCF_004005905.1_ASM400590v1_genomic.fna/checkm_result
[2024-01-24 14:07:05,170] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:05,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:05,193] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:05,193] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:05,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005905.1_ASM400590v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:05,194] [INFO] Task started: Blastn
[2024-01-24 14:07:05,194] [INFO] Running command: blastn -query GCF_004005905.1_ASM400590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9a4ed96-110f-43a4-97ac-e4eba6e66b87/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005905.1_ASM400590v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:06,370] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:06,374] [INFO] Selected 8 target genomes.
[2024-01-24 14:07:06,374] [INFO] Target genome list was writen to GCF_004005905.1_ASM400590v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:06,383] [INFO] Task started: fastANI
[2024-01-24 14:07:06,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg4854d8e9-3710-444f-8394-86303faf164e/GCF_004005905.1_ASM400590v1_genomic.fna.gz --refList GCF_004005905.1_ASM400590v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005905.1_ASM400590v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:14,850] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,863] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:14,863] [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_004005905.1	s__Novosphingobium umbonatum	100.0	1332	1335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012275515.1	s__Novosphingobium sp001898925	82.0545	863	1335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.48	97.63	0.91	0.85	4	-
GCF_014196525.1	s__Novosphingobium sediminicola	81.9257	868	1335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149295.1	s__Novosphingobium sp013149295	81.8909	847	1335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909235.1	s__Novosphingobium sp009909235	81.334	689	1335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336765.1	s__Novosphingobium sp002336765	80.6679	439	1335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598555.1	s__Novosphingobium rosa	79.7089	599	1335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017163935.1	s__Novosphingobium sp017163935	79.6617	607	1335	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,865] [INFO] GTDB search result was written to GCF_004005905.1_ASM400590v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:14,865] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:14,868] [INFO] DFAST_QC result json was written to GCF_004005905.1_ASM400590v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:14,869] [INFO] DFAST_QC completed!
[2024-01-24 14:07:14,869] [INFO] Total running time: 0h1m21s