[2024-01-25 19:35:06,142] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:06,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:06,144] [INFO] DQC Reference Directory: /var/lib/cwl/stge808e3ec-895f-4894-9d11-44faa70a25eb/dqc_reference
[2024-01-25 19:35:07,268] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:07,269] [INFO] Task started: Prodigal
[2024-01-25 19:35:07,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg0638b606-c644-48b9-b3dd-6c62e7fa9dad/GCF_012927405.1_ASM1292740v1_genomic.fna.gz | prodigal -d GCF_012927405.1_ASM1292740v1_genomic.fna/cds.fna -a GCF_012927405.1_ASM1292740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:19,866] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:19,866] [INFO] Task started: HMMsearch
[2024-01-25 19:35:19,866] [INFO] Running command: hmmsearch --tblout GCF_012927405.1_ASM1292740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge808e3ec-895f-4894-9d11-44faa70a25eb/dqc_reference/reference_markers.hmm GCF_012927405.1_ASM1292740v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:20,146] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:20,147] [INFO] Found 6/6 markers.
[2024-01-25 19:35:20,185] [INFO] Query marker FASTA was written to GCF_012927405.1_ASM1292740v1_genomic.fna/markers.fasta
[2024-01-25 19:35:20,185] [INFO] Task started: Blastn
[2024-01-25 19:35:20,185] [INFO] Running command: blastn -query GCF_012927405.1_ASM1292740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge808e3ec-895f-4894-9d11-44faa70a25eb/dqc_reference/reference_markers.fasta -out GCF_012927405.1_ASM1292740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:21,116] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:21,119] [INFO] Selected 12 target genomes.
[2024-01-25 19:35:21,119] [INFO] Target genome list was writen to GCF_012927405.1_ASM1292740v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:21,124] [INFO] Task started: fastANI
[2024-01-25 19:35:21,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg0638b606-c644-48b9-b3dd-6c62e7fa9dad/GCF_012927405.1_ASM1292740v1_genomic.fna.gz --refList GCF_012927405.1_ASM1292740v1_genomic.fna/target_genomes.txt --output GCF_012927405.1_ASM1292740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:31,768] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:31,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge808e3ec-895f-4894-9d11-44faa70a25eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:31,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge808e3ec-895f-4894-9d11-44faa70a25eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:31,777] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:35:31,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:31,777] [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 olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	100.0	1537	1540	95	conclusive
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	87.3951	928	1540	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	85.2058	957	1540	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	82.5396	694	1540	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	81.8287	682	1540	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	81.7767	673	1540	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	81.5954	672	1540	95	below_threshold
Novosphingobium sediminis	strain=NBRC 106119	GCA_007991615.1	707214	707214	type	True	80.7267	657	1540	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	80.4078	623	1540	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.9156	446	1540	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.713	403	1540	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.6353	393	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:31,779] [INFO] DFAST Taxonomy check result was written to GCF_012927405.1_ASM1292740v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:31,781] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:31,782] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:31,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge808e3ec-895f-4894-9d11-44faa70a25eb/dqc_reference/checkm_data
[2024-01-25 19:35:31,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:31,829] [INFO] Task started: CheckM
[2024-01-25 19:35:31,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012927405.1_ASM1292740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012927405.1_ASM1292740v1_genomic.fna/checkm_input GCF_012927405.1_ASM1292740v1_genomic.fna/checkm_result
[2024-01-25 19:36:11,845] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:11,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:11,864] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:11,864] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:11,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012927405.1_ASM1292740v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:11,865] [INFO] Task started: Blastn
[2024-01-25 19:36:11,865] [INFO] Running command: blastn -query GCF_012927405.1_ASM1292740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge808e3ec-895f-4894-9d11-44faa70a25eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_012927405.1_ASM1292740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:13,651] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:13,654] [INFO] Selected 14 target genomes.
[2024-01-25 19:36:13,654] [INFO] Target genome list was writen to GCF_012927405.1_ASM1292740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:13,662] [INFO] Task started: fastANI
[2024-01-25 19:36:13,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg0638b606-c644-48b9-b3dd-6c62e7fa9dad/GCF_012927405.1_ASM1292740v1_genomic.fna.gz --refList GCF_012927405.1_ASM1292740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012927405.1_ASM1292740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:27,346] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:27,357] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:27,357] [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_012927405.1	s__Novosphingobium olei	100.0	1538	1540	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_000013325.1	s__Novosphingobium aromaticivorans	82.5573	694	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000807925.1	s__Novosphingobium subterraneum	81.8568	680	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.63	97.57	0.88	0.77	4	-
GCF_001014975.1	s__Novosphingobium sp002336885	81.6306	674	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCF_015694345.1	s__Novosphingobium jiangmenense	81.6067	671	1540	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	81.5794	668	1540	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	81.4342	655	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003454795.1	s__Novosphingobium sp003454795	81.224	659	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_900176395.1	s__Novosphingobium sp900176395	81.0705	607	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991615.1	s__Novosphingobium sediminis	80.7364	656	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364785.1	s__Novosphingobium sp004364785	80.5427	599	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196055.1	s__Novosphingobium hassiacum	80.5	586	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641335.1	s__Novosphingobium sp012641335	80.425	592	1540	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	80.4112	623	1540	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 19:36:27,359] [INFO] GTDB search result was written to GCF_012927405.1_ASM1292740v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:27,359] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:27,362] [INFO] DFAST_QC result json was written to GCF_012927405.1_ASM1292740v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:27,363] [INFO] DFAST_QC completed!
[2024-01-25 19:36:27,363] [INFO] Total running time: 0h1m21s