[2024-01-24 13:54:04,327] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:04,330] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:04,330] [INFO] DQC Reference Directory: /var/lib/cwl/stg5266fb52-0004-4984-9a42-a7806278959a/dqc_reference
[2024-01-24 13:54:05,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:05,814] [INFO] Task started: Prodigal
[2024-01-24 13:54:05,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg0691e11a-ade9-4d24-b3b5-7e84350085f6/GCF_007846085.1_ASM784608v1_genomic.fna.gz | prodigal -d GCF_007846085.1_ASM784608v1_genomic.fna/cds.fna -a GCF_007846085.1_ASM784608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:25,511] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:25,511] [INFO] Task started: HMMsearch
[2024-01-24 13:54:25,511] [INFO] Running command: hmmsearch --tblout GCF_007846085.1_ASM784608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5266fb52-0004-4984-9a42-a7806278959a/dqc_reference/reference_markers.hmm GCF_007846085.1_ASM784608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:25,872] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:25,873] [INFO] Found 6/6 markers.
[2024-01-24 13:54:25,918] [INFO] Query marker FASTA was written to GCF_007846085.1_ASM784608v1_genomic.fna/markers.fasta
[2024-01-24 13:54:25,919] [INFO] Task started: Blastn
[2024-01-24 13:54:25,919] [INFO] Running command: blastn -query GCF_007846085.1_ASM784608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5266fb52-0004-4984-9a42-a7806278959a/dqc_reference/reference_markers.fasta -out GCF_007846085.1_ASM784608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:26,610] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:26,613] [INFO] Selected 19 target genomes.
[2024-01-24 13:54:26,613] [INFO] Target genome list was writen to GCF_007846085.1_ASM784608v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:26,645] [INFO] Task started: fastANI
[2024-01-24 13:54:26,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg0691e11a-ade9-4d24-b3b5-7e84350085f6/GCF_007846085.1_ASM784608v1_genomic.fna.gz --refList GCF_007846085.1_ASM784608v1_genomic.fna/target_genomes.txt --output GCF_007846085.1_ASM784608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:54:45,015] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:45,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5266fb52-0004-4984-9a42-a7806278959a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:54:45,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5266fb52-0004-4984-9a42-a7806278959a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:54:45,032] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:54:45,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:54:45,033] [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
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	100.0	1409	1409	95	conclusive
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	78.9508	399	1409	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	78.8549	492	1409	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	78.4799	485	1409	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	78.4755	462	1409	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	78.4231	490	1409	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	78.4025	471	1409	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	78.2691	430	1409	95	below_threshold
Mucilaginibacter terrenus	strain=ZH6	GCA_003432065.1	2482727	2482727	type	True	78.1672	319	1409	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	78.1234	394	1409	95	below_threshold
Mucilaginibacter psychrotolerans	strain=NH7-4	GCA_004519315.1	1524096	1524096	type	True	78.0514	366	1409	95	below_threshold
Mucilaginibacter auburnensis	strain=DSM 28175	GCA_002797815.1	1457233	1457233	type	True	77.9779	213	1409	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.8204	305	1409	95	below_threshold
Mucilaginibacter segetis	strain=SD-g	GCA_016522075.1	2793071	2793071	type	True	77.8096	293	1409	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.7969	323	1409	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	77.7886	223	1409	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.5942	262	1409	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	77.4882	284	1409	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.4663	280	1409	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:54:45,034] [INFO] DFAST Taxonomy check result was written to GCF_007846085.1_ASM784608v1_genomic.fna/tc_result.tsv
[2024-01-24 13:54:45,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:54:45,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:54:45,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5266fb52-0004-4984-9a42-a7806278959a/dqc_reference/checkm_data
[2024-01-24 13:54:45,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:54:45,080] [INFO] Task started: CheckM
[2024-01-24 13:54:45,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007846085.1_ASM784608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007846085.1_ASM784608v1_genomic.fna/checkm_input GCF_007846085.1_ASM784608v1_genomic.fna/checkm_result
[2024-01-24 13:55:39,780] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:39,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:39,824] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:39,825] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:39,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007846085.1_ASM784608v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:39,826] [INFO] Task started: Blastn
[2024-01-24 13:55:39,826] [INFO] Running command: blastn -query GCF_007846085.1_ASM784608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5266fb52-0004-4984-9a42-a7806278959a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007846085.1_ASM784608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:40,668] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:40,672] [INFO] Selected 20 target genomes.
[2024-01-24 13:55:40,673] [INFO] Target genome list was writen to GCF_007846085.1_ASM784608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:40,707] [INFO] Task started: fastANI
[2024-01-24 13:55:40,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg0691e11a-ade9-4d24-b3b5-7e84350085f6/GCF_007846085.1_ASM784608v1_genomic.fna.gz --refList GCF_007846085.1_ASM784608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007846085.1_ASM784608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:59,487] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:59,504] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:59,504] [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_007846085.1	s__Mucilaginibacter sp007846085	100.0	1409	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007846095.1	s__Mucilaginibacter sp007846095	78.9332	401	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432115.1	s__Mucilaginibacter sp003432115	78.8728	489	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635105.1	s__Mucilaginibacter sp003635105	78.7244	490	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636615.1	s__Mucilaginibacter sp001636615	78.5573	487	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938025.2	s__Mucilaginibacter sp005938025	78.527	452	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168255.1	s__Mucilaginibacter terrigena	78.4706	462	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013915.1	s__Mucilaginibacter pedocola	78.3981	472	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288635.1	s__Mucilaginibacter sp002288635	78.3823	378	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773275.1	s__Mucilaginibacter rigui	78.3333	488	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432065.1	s__Mucilaginibacter sp003432065	78.1672	319	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004054195.1	s__Mucilaginibacter sp004054195	78.128	394	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519315.1	s__Mucilaginibacter psychrotolerans	78.0561	365	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797815.1	s__Mucilaginibacter auburnensis	77.9779	213	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001596135.1	s__Mucilaginibacter sp001596135	77.9616	333	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093045.1	s__Mucilaginibacter sp010093045	77.9574	420	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_900101875.1	s__Mucilaginibacter pineti	77.7969	323	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005815.1	s__Mucilaginibacter limnophilus	77.7879	223	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223065.1	s__Mucilaginibacter sp015223065	77.6347	275	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001705515.1	s__Mucilaginibacter sp001705515	77.2266	166	1409	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:59,507] [INFO] GTDB search result was written to GCF_007846085.1_ASM784608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:59,507] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:59,512] [INFO] DFAST_QC result json was written to GCF_007846085.1_ASM784608v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:59,513] [INFO] DFAST_QC completed!
[2024-01-24 13:55:59,513] [INFO] Total running time: 0h1m55s