[2024-01-24 11:43:41,903] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:41,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:41,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg399a6e21-c3e4-43e4-952c-ee8510631a4c/dqc_reference
[2024-01-24 11:43:43,413] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,414] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,414] [INFO] Running command: gunzip -c /var/lib/cwl/stga4b3561e-1583-4d37-a5f2-89a72df122a8/GCF_002813245.1_ASM281324v1_genomic.fna.gz | prodigal -d GCF_002813245.1_ASM281324v1_genomic.fna/cds.fna -a GCF_002813245.1_ASM281324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:53,652] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:53,652] [INFO] Task started: HMMsearch
[2024-01-24 11:43:53,652] [INFO] Running command: hmmsearch --tblout GCF_002813245.1_ASM281324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg399a6e21-c3e4-43e4-952c-ee8510631a4c/dqc_reference/reference_markers.hmm GCF_002813245.1_ASM281324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:53,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:53,980] [INFO] Found 6/6 markers.
[2024-01-24 11:43:54,024] [INFO] Query marker FASTA was written to GCF_002813245.1_ASM281324v1_genomic.fna/markers.fasta
[2024-01-24 11:43:54,024] [INFO] Task started: Blastn
[2024-01-24 11:43:54,024] [INFO] Running command: blastn -query GCF_002813245.1_ASM281324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg399a6e21-c3e4-43e4-952c-ee8510631a4c/dqc_reference/reference_markers.fasta -out GCF_002813245.1_ASM281324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:55,019] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:55,022] [INFO] Selected 18 target genomes.
[2024-01-24 11:43:55,022] [INFO] Target genome list was writen to GCF_002813245.1_ASM281324v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:55,029] [INFO] Task started: fastANI
[2024-01-24 11:43:55,029] [INFO] Running command: fastANI --query /var/lib/cwl/stga4b3561e-1583-4d37-a5f2-89a72df122a8/GCF_002813245.1_ASM281324v1_genomic.fna.gz --refList GCF_002813245.1_ASM281324v1_genomic.fna/target_genomes.txt --output GCF_002813245.1_ASM281324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:11,078] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:11,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg399a6e21-c3e4-43e4-952c-ee8510631a4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:11,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg399a6e21-c3e4-43e4-952c-ee8510631a4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:11,092] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:11,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:11,093] [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 kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	100.0	1161	1161	95	conclusive
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	80.6299	594	1161	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	80.5803	530	1161	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	80.4978	535	1161	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	80.2872	511	1161	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	80.1957	482	1161	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	80.157	513	1161	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	80.1423	479	1161	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.9593	531	1161	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	79.571	486	1161	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	79.4571	427	1161	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	79.272	450	1161	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.9663	414	1161	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	78.8788	394	1161	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.8666	390	1161	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.8416	446	1161	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.8023	389	1161	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.8	380	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:11,095] [INFO] DFAST Taxonomy check result was written to GCF_002813245.1_ASM281324v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:11,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:11,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:11,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg399a6e21-c3e4-43e4-952c-ee8510631a4c/dqc_reference/checkm_data
[2024-01-24 11:44:11,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:11,138] [INFO] Task started: CheckM
[2024-01-24 11:44:11,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002813245.1_ASM281324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002813245.1_ASM281324v1_genomic.fna/checkm_input GCF_002813245.1_ASM281324v1_genomic.fna/checkm_result
[2024-01-24 11:44:45,790] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:45,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:45,809] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:45,810] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:45,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002813245.1_ASM281324v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:45,811] [INFO] Task started: Blastn
[2024-01-24 11:44:45,811] [INFO] Running command: blastn -query GCF_002813245.1_ASM281324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg399a6e21-c3e4-43e4-952c-ee8510631a4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002813245.1_ASM281324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:47,567] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:47,571] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:47,571] [INFO] Target genome list was writen to GCF_002813245.1_ASM281324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:47,619] [INFO] Task started: fastANI
[2024-01-24 11:44:47,619] [INFO] Running command: fastANI --query /var/lib/cwl/stga4b3561e-1583-4d37-a5f2-89a72df122a8/GCF_002813245.1_ASM281324v1_genomic.fna.gz --refList GCF_002813245.1_ASM281324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002813245.1_ASM281324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:56,601] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:56,617] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:56,617] [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_002813245.1	s__Novosphingobium kunmingense	100.0	1161	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018241045.1	s__Novosphingobium sp018241045	82.1692	468	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	81.3824	613	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141325.1	s__Novosphingobium sp013141325	81.3172	460	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719755.1	s__Novosphingobium sp016719755	81.2919	598	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.59	99.59	0.90	0.90	2	-
GCA_015657645.1	s__Novosphingobium sp015657645	80.9098	480	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652615.1	s__Novosphingobium arvoryzae	80.6299	594	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954425.1	s__Novosphingobium ginsenosidimutans	80.5011	534	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240895.1	s__Novosphingobium sp018240895	80.4677	507	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018334165.1	s__Novosphingobium sp018334165	80.435	494	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_009926135.1	s__Novosphingobium sp009926135	80.4348	545	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822005.1	s__Novosphingobium sp013822005	80.2407	439	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198665.1	s__Novosphingobium sp002198665	80.0802	521	1161	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 11:44:56,619] [INFO] GTDB search result was written to GCF_002813245.1_ASM281324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:56,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:56,623] [INFO] DFAST_QC result json was written to GCF_002813245.1_ASM281324v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:56,623] [INFO] DFAST_QC completed!
[2024-01-24 11:44:56,623] [INFO] Total running time: 0h1m15s