[2024-01-24 13:01:53,109] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:53,111] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:53,111] [INFO] DQC Reference Directory: /var/lib/cwl/stg965c9ee8-e626-4acb-9d90-23ec8de2440f/dqc_reference
[2024-01-24 13:01:54,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,425] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,425] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfa3a8b0-fb9f-47d9-a96d-1f5a8bce13df/GCF_009909235.1_ASM990923v1_genomic.fna.gz | prodigal -d GCF_009909235.1_ASM990923v1_genomic.fna/cds.fna -a GCF_009909235.1_ASM990923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:06,775] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:06,775] [INFO] Task started: HMMsearch
[2024-01-24 13:02:06,775] [INFO] Running command: hmmsearch --tblout GCF_009909235.1_ASM990923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg965c9ee8-e626-4acb-9d90-23ec8de2440f/dqc_reference/reference_markers.hmm GCF_009909235.1_ASM990923v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:07,104] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:07,105] [INFO] Found 6/6 markers.
[2024-01-24 13:02:07,177] [INFO] Query marker FASTA was written to GCF_009909235.1_ASM990923v1_genomic.fna/markers.fasta
[2024-01-24 13:02:07,178] [INFO] Task started: Blastn
[2024-01-24 13:02:07,178] [INFO] Running command: blastn -query GCF_009909235.1_ASM990923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg965c9ee8-e626-4acb-9d90-23ec8de2440f/dqc_reference/reference_markers.fasta -out GCF_009909235.1_ASM990923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:08,163] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:08,166] [INFO] Selected 15 target genomes.
[2024-01-24 13:02:08,167] [INFO] Target genome list was writen to GCF_009909235.1_ASM990923v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:08,171] [INFO] Task started: fastANI
[2024-01-24 13:02:08,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfa3a8b0-fb9f-47d9-a96d-1f5a8bce13df/GCF_009909235.1_ASM990923v1_genomic.fna.gz --refList GCF_009909235.1_ASM990923v1_genomic.fna/target_genomes.txt --output GCF_009909235.1_ASM990923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:19,963] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:19,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg965c9ee8-e626-4acb-9d90-23ec8de2440f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:19,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg965c9ee8-e626-4acb-9d90-23ec8de2440f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:19,979] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:19,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:19,980] [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 ovatum	strain=FSY-8	GCA_009909235.1	1908523	1908523	type	True	100.0	1188	1188	95	conclusive
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	81.1921	688	1188	95	below_threshold
Novosphingobium sediminicola	strain=DSM 27057	GCA_014196525.1	563162	563162	type	True	81.1789	740	1188	95	below_threshold
Novosphingobium rosa	strain=NBRC 15208	GCA_001598555.1	76978	76978	type	True	79.873	571	1188	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	79.2326	473	1188	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.0553	420	1188	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.828	439	1188	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	78.8165	383	1188	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.7792	355	1188	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.6624	384	1188	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	78.504	391	1188	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	78.501	381	1188	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	77.9175	276	1188	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.5793	154	1188	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.2067	183	1188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:19,982] [INFO] DFAST Taxonomy check result was written to GCF_009909235.1_ASM990923v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:19,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:19,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:19,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg965c9ee8-e626-4acb-9d90-23ec8de2440f/dqc_reference/checkm_data
[2024-01-24 13:02:19,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:20,020] [INFO] Task started: CheckM
[2024-01-24 13:02:20,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009909235.1_ASM990923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009909235.1_ASM990923v1_genomic.fna/checkm_input GCF_009909235.1_ASM990923v1_genomic.fna/checkm_result
[2024-01-24 13:03:01,056] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:01,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:01,083] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:01,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:01,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009909235.1_ASM990923v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:01,085] [INFO] Task started: Blastn
[2024-01-24 13:03:01,085] [INFO] Running command: blastn -query GCF_009909235.1_ASM990923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg965c9ee8-e626-4acb-9d90-23ec8de2440f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009909235.1_ASM990923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:02,792] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:02,797] [INFO] Selected 10 target genomes.
[2024-01-24 13:03:02,797] [INFO] Target genome list was writen to GCF_009909235.1_ASM990923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:02,809] [INFO] Task started: fastANI
[2024-01-24 13:03:02,809] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfa3a8b0-fb9f-47d9-a96d-1f5a8bce13df/GCF_009909235.1_ASM990923v1_genomic.fna.gz --refList GCF_009909235.1_ASM990923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009909235.1_ASM990923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:12,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:12,148] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:12,148] [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_009909235.1	s__Novosphingobium sp009909235	100.0	1188	1188	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_014196525.1	s__Novosphingobium sediminicola	81.2296	734	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005905.1	s__Novosphingobium umbonatum	81.2251	684	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275515.1	s__Novosphingobium sp001898925	81.1526	743	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.48	97.63	0.91	0.85	4	-
GCF_013149295.1	s__Novosphingobium sp013149295	81.0565	736	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208375.1	s__Novosphingobium sp003208375	80.2352	604	1188	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	80.0587	406	1188	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	79.9387	555	1188	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	79.8819	570	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903911985.1	s__Novosphingobium sp903911985	78.3509	257	1188	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 13:03:12,150] [INFO] GTDB search result was written to GCF_009909235.1_ASM990923v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:12,151] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:12,157] [INFO] DFAST_QC result json was written to GCF_009909235.1_ASM990923v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:12,157] [INFO] DFAST_QC completed!
[2024-01-24 13:03:12,157] [INFO] Total running time: 0h1m19s