[2024-01-24 13:22:10,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgc67b8b4f-234f-406d-b57d-5076ef2c505c/dqc_reference
[2024-01-24 13:22:11,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,970] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,971] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5ddfe13-6d74-4024-b6d4-4ff627c7fafd/GCF_012849215.1_ASM1284921v1_genomic.fna.gz | prodigal -d GCF_012849215.1_ASM1284921v1_genomic.fna/cds.fna -a GCF_012849215.1_ASM1284921v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:33,587] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:33,588] [INFO] Task started: HMMsearch
[2024-01-24 13:22:33,588] [INFO] Running command: hmmsearch --tblout GCF_012849215.1_ASM1284921v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc67b8b4f-234f-406d-b57d-5076ef2c505c/dqc_reference/reference_markers.hmm GCF_012849215.1_ASM1284921v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:33,926] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:33,927] [INFO] Found 6/6 markers.
[2024-01-24 13:22:33,969] [INFO] Query marker FASTA was written to GCF_012849215.1_ASM1284921v1_genomic.fna/markers.fasta
[2024-01-24 13:22:33,969] [INFO] Task started: Blastn
[2024-01-24 13:22:33,969] [INFO] Running command: blastn -query GCF_012849215.1_ASM1284921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc67b8b4f-234f-406d-b57d-5076ef2c505c/dqc_reference/reference_markers.fasta -out GCF_012849215.1_ASM1284921v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:34,594] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:34,597] [INFO] Selected 22 target genomes.
[2024-01-24 13:22:34,597] [INFO] Target genome list was writen to GCF_012849215.1_ASM1284921v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:34,607] [INFO] Task started: fastANI
[2024-01-24 13:22:34,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5ddfe13-6d74-4024-b6d4-4ff627c7fafd/GCF_012849215.1_ASM1284921v1_genomic.fna.gz --refList GCF_012849215.1_ASM1284921v1_genomic.fna/target_genomes.txt --output GCF_012849215.1_ASM1284921v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:57,039] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:57,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc67b8b4f-234f-406d-b57d-5076ef2c505c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:57,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc67b8b4f-234f-406d-b57d-5076ef2c505c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:57,057] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:57,057] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:57,057] [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 robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	100.0	1660	1661	95	conclusive
Mucilaginibacter aquatilis	strain=HME9299	GCA_009755275.1	1517760	1517760	type	True	78.0712	268	1661	95	below_threshold
Mucilaginibacter galii	strain=CCM 8711	GCA_014635825.1	2005073	2005073	type	True	78.0102	310	1661	95	below_threshold
Mucilaginibacter auburnensis	strain=DSM 28175	GCA_002797815.1	1457233	1457233	type	True	77.6936	153	1661	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.4817	205	1661	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	77.4314	191	1661	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.4152	203	1661	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.3337	186	1661	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.2622	157	1661	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	77.1289	166	1661	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.0305	169	1661	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	77.0292	60	1661	95	below_threshold
Mucilaginibacter terrenus	strain=ZH6	GCA_003432065.1	2482727	2482727	type	True	77.0208	130	1661	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	77.0104	167	1661	95	below_threshold
Mucilaginibacter boryungensis	strain=KCTC 23157	GCA_015221995.1	768480	768480	type	True	76.951	178	1661	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	76.893	163	1661	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	76.8446	185	1661	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	76.8327	150	1661	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	76.7689	141	1661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:57,059] [INFO] DFAST Taxonomy check result was written to GCF_012849215.1_ASM1284921v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:57,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:57,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:57,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc67b8b4f-234f-406d-b57d-5076ef2c505c/dqc_reference/checkm_data
[2024-01-24 13:22:57,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:57,118] [INFO] Task started: CheckM
[2024-01-24 13:22:57,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012849215.1_ASM1284921v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012849215.1_ASM1284921v1_genomic.fna/checkm_input GCF_012849215.1_ASM1284921v1_genomic.fna/checkm_result
[2024-01-24 13:23:56,539] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:56,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:56,563] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:56,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:56,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012849215.1_ASM1284921v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:56,564] [INFO] Task started: Blastn
[2024-01-24 13:23:56,564] [INFO] Running command: blastn -query GCF_012849215.1_ASM1284921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc67b8b4f-234f-406d-b57d-5076ef2c505c/dqc_reference/reference_markers_gtdb.fasta -out GCF_012849215.1_ASM1284921v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:57,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:57,399] [INFO] Selected 19 target genomes.
[2024-01-24 13:23:57,400] [INFO] Target genome list was writen to GCF_012849215.1_ASM1284921v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:57,443] [INFO] Task started: fastANI
[2024-01-24 13:23:57,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5ddfe13-6d74-4024-b6d4-4ff627c7fafd/GCF_012849215.1_ASM1284921v1_genomic.fna.gz --refList GCF_012849215.1_ASM1284921v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012849215.1_ASM1284921v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:12,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:12,577] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:12,578] [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_012849215.1	s__Mucilaginibacter sp012849215	100.0	1660	1661	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_018390515.1	s__Mucilaginibacter sp018390515	78.2959	400	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009770985.1	s__Mucilaginibacter sp009770985	78.2686	426	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755275.1	s__Mucilaginibacter aquatilis	78.1031	265	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635825.1	s__Mucilaginibacter galii	78.0106	310	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576455.2	s__Mucilaginibacter celer	77.563	203	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846095.1	s__Mucilaginibacter sp007846095	77.2805	156	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001911425.1	s__Mucilaginibacter polytrichastri	77.2785	225	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013287375.1	s__Mucilaginibacter sp013287375	77.2408	95	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.48	99.44	0.60	0.60	3	-
GCA_903644075.1	s__Mucilaginibacter sp903644075	77.0982	164	1661	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	77.0534	154	1661	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	77.0389	129	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408825.1	s__Mucilaginibacter sp013408825	77.0353	139	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765905.1	s__Mucilaginibacter sp009765905	76.901	177	1661	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	76.8844	183	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205845.1	s__Mucilaginibacter sp014205845	76.7266	182	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286565.1	s__Mucilaginibacter sp013286565	76.6919	89	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903915155.1	s__Mucilaginibacter sp903915155	76.6893	125	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286325.1	s__Mucilaginibacter sp013286325	76.5934	87	1661	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 13:24:12,579] [INFO] GTDB search result was written to GCF_012849215.1_ASM1284921v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:12,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:12,584] [INFO] DFAST_QC result json was written to GCF_012849215.1_ASM1284921v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:12,584] [INFO] DFAST_QC completed!
[2024-01-24 13:24:12,584] [INFO] Total running time: 0h2m2s