[2024-01-25 19:37:20,619] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:20,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:20,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg58b3aba4-a25f-4f26-8197-961544310857/dqc_reference
[2024-01-25 19:37:21,709] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:21,709] [INFO] Task started: Prodigal
[2024-01-25 19:37:21,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg97d6df3b-c876-47e7-a8a5-ee4294183097/GCF_000375445.1_ASM37544v1_genomic.fna.gz | prodigal -d GCF_000375445.1_ASM37544v1_genomic.fna/cds.fna -a GCF_000375445.1_ASM37544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:32,994] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:32,994] [INFO] Task started: HMMsearch
[2024-01-25 19:37:32,994] [INFO] Running command: hmmsearch --tblout GCF_000375445.1_ASM37544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58b3aba4-a25f-4f26-8197-961544310857/dqc_reference/reference_markers.hmm GCF_000375445.1_ASM37544v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:33,220] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:33,221] [INFO] Found 6/6 markers.
[2024-01-25 19:37:33,258] [INFO] Query marker FASTA was written to GCF_000375445.1_ASM37544v1_genomic.fna/markers.fasta
[2024-01-25 19:37:33,258] [INFO] Task started: Blastn
[2024-01-25 19:37:33,258] [INFO] Running command: blastn -query GCF_000375445.1_ASM37544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58b3aba4-a25f-4f26-8197-961544310857/dqc_reference/reference_markers.fasta -out GCF_000375445.1_ASM37544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:34,119] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:34,122] [INFO] Selected 18 target genomes.
[2024-01-25 19:37:34,122] [INFO] Target genome list was writen to GCF_000375445.1_ASM37544v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:34,132] [INFO] Task started: fastANI
[2024-01-25 19:37:34,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d6df3b-c876-47e7-a8a5-ee4294183097/GCF_000375445.1_ASM37544v1_genomic.fna.gz --refList GCF_000375445.1_ASM37544v1_genomic.fna/target_genomes.txt --output GCF_000375445.1_ASM37544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:49,046] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:49,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58b3aba4-a25f-4f26-8197-961544310857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:49,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58b3aba4-a25f-4f26-8197-961544310857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:49,058] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:37:49,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:49,058] [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 nitrogenifigens	strain=DSM 19370	GCA_000375445.1	378548	378548	type	True	100.0	1357	1362	95	conclusive
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000192575.1	378548	378548	type	True	99.9633	1351	1362	95	conclusive
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	80.0623	571	1362	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.8726	505	1362	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.7867	497	1362	95	below_threshold
Novosphingobium capsulatum	strain=NBRC 12533	GCA_001598375.1	13688	13688	type	True	79.5258	526	1362	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	79.4808	426	1362	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	79.4293	504	1362	95	below_threshold
Novosphingobium acidiphilum	strain=DSM 19966	GCA_000429005.1	505248	505248	type	True	79.3069	575	1362	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	79.2136	444	1362	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	79.0955	426	1362	95	below_threshold
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	79.0009	454	1362	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	78.9107	444	1362	95	below_threshold
Novosphingobium meiothermophilum	strain=SYSU G00007	GCA_003171715.1	2202251	2202251	type	True	78.7667	397	1362	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	78.7207	383	1362	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.0262	323	1362	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.9629	262	1362	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	77.5082	232	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:49,059] [INFO] DFAST Taxonomy check result was written to GCF_000375445.1_ASM37544v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:49,059] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:49,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:49,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58b3aba4-a25f-4f26-8197-961544310857/dqc_reference/checkm_data
[2024-01-25 19:37:49,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:49,100] [INFO] Task started: CheckM
[2024-01-25 19:37:49,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000375445.1_ASM37544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000375445.1_ASM37544v1_genomic.fna/checkm_input GCF_000375445.1_ASM37544v1_genomic.fna/checkm_result
[2024-01-25 19:38:29,309] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:29,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:29,326] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:29,326] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:29,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000375445.1_ASM37544v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:29,327] [INFO] Task started: Blastn
[2024-01-25 19:38:29,327] [INFO] Running command: blastn -query GCF_000375445.1_ASM37544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58b3aba4-a25f-4f26-8197-961544310857/dqc_reference/reference_markers_gtdb.fasta -out GCF_000375445.1_ASM37544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:31,013] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:31,016] [INFO] Selected 14 target genomes.
[2024-01-25 19:38:31,016] [INFO] Target genome list was writen to GCF_000375445.1_ASM37544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:31,039] [INFO] Task started: fastANI
[2024-01-25 19:38:31,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d6df3b-c876-47e7-a8a5-ee4294183097/GCF_000375445.1_ASM37544v1_genomic.fna.gz --refList GCF_000375445.1_ASM37544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000375445.1_ASM37544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:43,486] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:43,498] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:43,498] [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_000192575.1	s__Novosphingobium nitrogenifigens	99.9633	1351	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_001519055.1	s__Novosphingobium sp001519055	81.109	748	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661825.1	s__Novosphingobium capsulatum_A	80.5251	513	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652855.1	s__Novosphingobium pokkalii	80.0725	570	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001519065.1	s__Novosphingobium sp001519065	79.9451	677	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005145025.1	s__Novosphingobium sp005145025	79.6919	517	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014975.1	s__Novosphingobium sp002336885	79.6372	520	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCF_003208305.1	s__Novosphingobium sp003208305	79.5169	494	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725355.1	s__Novosphingobium sp001725355	79.5038	462	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013325.1	s__Novosphingobium aromaticivorans	79.469	427	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903832325.1	s__Novosphingobium sp903832325	79.4659	605	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.98	99.94	0.97	0.96	4	-
GCF_012927405.1	s__Novosphingobium olei	79.447	503	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001519075.1	s__Novosphingobium fuchskuhlense	78.9056	445	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893935.1	s__Novosphingobium sp903893935	78.6562	301	1362	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 19:38:43,499] [INFO] GTDB search result was written to GCF_000375445.1_ASM37544v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:43,500] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:43,503] [INFO] DFAST_QC result json was written to GCF_000375445.1_ASM37544v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:43,503] [INFO] DFAST_QC completed!
[2024-01-25 19:38:43,503] [INFO] Total running time: 0h1m23s