[2024-01-24 15:10:54,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,335] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg711a2cb2-93e1-4071-be5e-e18ed34ade2a/dqc_reference
[2024-01-24 15:10:56,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,633] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a056ddb-028a-48fe-87ca-f2a20e078e55/GCF_007846095.1_ASM784609v1_genomic.fna.gz | prodigal -d GCF_007846095.1_ASM784609v1_genomic.fna/cds.fna -a GCF_007846095.1_ASM784609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:16,470] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:16,470] [INFO] Task started: HMMsearch
[2024-01-24 15:11:16,470] [INFO] Running command: hmmsearch --tblout GCF_007846095.1_ASM784609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg711a2cb2-93e1-4071-be5e-e18ed34ade2a/dqc_reference/reference_markers.hmm GCF_007846095.1_ASM784609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:16,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:16,799] [INFO] Found 6/6 markers.
[2024-01-24 15:11:16,845] [INFO] Query marker FASTA was written to GCF_007846095.1_ASM784609v1_genomic.fna/markers.fasta
[2024-01-24 15:11:16,846] [INFO] Task started: Blastn
[2024-01-24 15:11:16,846] [INFO] Running command: blastn -query GCF_007846095.1_ASM784609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg711a2cb2-93e1-4071-be5e-e18ed34ade2a/dqc_reference/reference_markers.fasta -out GCF_007846095.1_ASM784609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:17,527] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:17,531] [INFO] Selected 18 target genomes.
[2024-01-24 15:11:17,532] [INFO] Target genome list was writen to GCF_007846095.1_ASM784609v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:17,554] [INFO] Task started: fastANI
[2024-01-24 15:11:17,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a056ddb-028a-48fe-87ca-f2a20e078e55/GCF_007846095.1_ASM784609v1_genomic.fna.gz --refList GCF_007846095.1_ASM784609v1_genomic.fna/target_genomes.txt --output GCF_007846095.1_ASM784609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:33,986] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:33,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg711a2cb2-93e1-4071-be5e-e18ed34ade2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:33,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg711a2cb2-93e1-4071-be5e-e18ed34ade2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:34,010] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:34,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:34,010] [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 achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	100.0	1417	1418	95	conclusive
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	82.1045	929	1418	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	79.0627	395	1418	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	78.5686	511	1418	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	78.5172	538	1418	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	78.4573	543	1418	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	78.454	546	1418	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	78.2333	440	1418	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	78.1205	381	1418	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	78.0796	385	1418	95	below_threshold
Mucilaginibacter terrenus	strain=ZH6	GCA_003432065.1	2482727	2482727	type	True	78.0058	309	1418	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	77.7971	223	1418	95	below_threshold
Mucilaginibacter segetis	strain=SD-g	GCA_016522075.1	2793071	2793071	type	True	77.7766	279	1418	95	below_threshold
Mucilaginibacter psychrotolerans	strain=NH7-4	GCA_004519315.1	1524096	1524096	type	True	77.7728	337	1418	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.6651	329	1418	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.421	261	1418	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.3406	237	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:34,012] [INFO] DFAST Taxonomy check result was written to GCF_007846095.1_ASM784609v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:34,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:34,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:34,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg711a2cb2-93e1-4071-be5e-e18ed34ade2a/dqc_reference/checkm_data
[2024-01-24 15:11:34,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:34,065] [INFO] Task started: CheckM
[2024-01-24 15:11:34,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007846095.1_ASM784609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007846095.1_ASM784609v1_genomic.fna/checkm_input GCF_007846095.1_ASM784609v1_genomic.fna/checkm_result
[2024-01-24 15:12:27,820] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:27,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:27,843] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:27,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:27,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007846095.1_ASM784609v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:27,844] [INFO] Task started: Blastn
[2024-01-24 15:12:27,844] [INFO] Running command: blastn -query GCF_007846095.1_ASM784609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg711a2cb2-93e1-4071-be5e-e18ed34ade2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007846095.1_ASM784609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:28,656] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:28,660] [INFO] Selected 11 target genomes.
[2024-01-24 15:12:28,660] [INFO] Target genome list was writen to GCF_007846095.1_ASM784609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:28,669] [INFO] Task started: fastANI
[2024-01-24 15:12:28,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a056ddb-028a-48fe-87ca-f2a20e078e55/GCF_007846095.1_ASM784609v1_genomic.fna.gz --refList GCF_007846095.1_ASM784609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007846095.1_ASM784609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:38,938] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:38,953] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:38,953] [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_007846095.1	s__Mucilaginibacter sp007846095	100.0	1417	1418	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_003432115.1	s__Mucilaginibacter sp003432115	82.1207	927	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763755.1	s__Mucilaginibacter sp016763755	81.6193	771	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898335.1	s__Mucilaginibacter sp001898335	81.0928	712	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.32	99.30	0.92	0.89	3	-
GCF_002288635.1	s__Mucilaginibacter sp002288635	81.0844	714	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846085.1	s__Mucilaginibacter sp007846085	79.0518	396	1418	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	78.7166	546	1418	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	78.5605	511	1418	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	77.7971	223	1418	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	77.7728	337	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903642215.1	s__Mucilaginibacter_A sp903642215	75.7375	87	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:38,955] [INFO] GTDB search result was written to GCF_007846095.1_ASM784609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:38,956] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:38,960] [INFO] DFAST_QC result json was written to GCF_007846095.1_ASM784609v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:38,960] [INFO] DFAST_QC completed!
[2024-01-24 15:12:38,960] [INFO] Total running time: 0h1m45s