[2024-01-24 13:58:11,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:11,102] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:11,102] [INFO] DQC Reference Directory: /var/lib/cwl/stg466137e8-b3c3-4ec7-83e2-88947d0cefaf/dqc_reference
[2024-01-24 13:58:12,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,417] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg4791de54-584f-4547-911b-4b722ebda85e/GCF_015222005.1_ASM1522200v1_genomic.fna.gz | prodigal -d GCF_015222005.1_ASM1522200v1_genomic.fna/cds.fna -a GCF_015222005.1_ASM1522200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:36,810] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:36,810] [INFO] Task started: HMMsearch
[2024-01-24 13:58:36,811] [INFO] Running command: hmmsearch --tblout GCF_015222005.1_ASM1522200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg466137e8-b3c3-4ec7-83e2-88947d0cefaf/dqc_reference/reference_markers.hmm GCF_015222005.1_ASM1522200v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:37,190] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:37,194] [INFO] Found 6/6 markers.
[2024-01-24 13:58:37,243] [INFO] Query marker FASTA was written to GCF_015222005.1_ASM1522200v1_genomic.fna/markers.fasta
[2024-01-24 13:58:37,244] [INFO] Task started: Blastn
[2024-01-24 13:58:37,244] [INFO] Running command: blastn -query GCF_015222005.1_ASM1522200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg466137e8-b3c3-4ec7-83e2-88947d0cefaf/dqc_reference/reference_markers.fasta -out GCF_015222005.1_ASM1522200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:37,864] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:37,868] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:37,869] [INFO] Target genome list was writen to GCF_015222005.1_ASM1522200v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:37,884] [INFO] Task started: fastANI
[2024-01-24 13:58:37,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg4791de54-584f-4547-911b-4b722ebda85e/GCF_015222005.1_ASM1522200v1_genomic.fna.gz --refList GCF_015222005.1_ASM1522200v1_genomic.fna/target_genomes.txt --output GCF_015222005.1_ASM1522200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:59,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:59,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg466137e8-b3c3-4ec7-83e2-88947d0cefaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:59,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg466137e8-b3c3-4ec7-83e2-88947d0cefaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:59,732] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:59,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:59,733] [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 myungsuensis	strain=KCTC 22746	GCA_015222005.1	649104	649104	type	True	100.0	1683	1683	95	conclusive
Mucilaginibacter mali	strain=G2-14	GCA_013283875.1	2740462	2740462	type	True	78.0726	526	1683	95	below_threshold
Mucilaginibacter boryungensis	strain=KCTC 23157	GCA_015221995.1	768480	768480	type	True	77.9467	369	1683	95	below_threshold
Mucilaginibacter yixingensis	strain=DSM 26809	GCA_003050755.1	1295612	1295612	type	True	77.5732	283	1683	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.5087	204	1683	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.4552	202	1683	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.3327	225	1683	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	77.277	235	1683	95	below_threshold
Mucilaginibacter galii	strain=CCM 8711	GCA_014635825.1	2005073	2005073	type	True	77.2	161	1683	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.1901	269	1683	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	77.0763	242	1683	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	77.0145	237	1683	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.0025	230	1683	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	76.972	242	1683	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	76.8404	234	1683	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	76.7481	167	1683	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	76.7356	161	1683	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	76.5903	224	1683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:59,735] [INFO] DFAST Taxonomy check result was written to GCF_015222005.1_ASM1522200v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:59,735] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:59,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:59,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg466137e8-b3c3-4ec7-83e2-88947d0cefaf/dqc_reference/checkm_data
[2024-01-24 13:58:59,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:59,792] [INFO] Task started: CheckM
[2024-01-24 13:58:59,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015222005.1_ASM1522200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015222005.1_ASM1522200v1_genomic.fna/checkm_input GCF_015222005.1_ASM1522200v1_genomic.fna/checkm_result
[2024-01-24 14:00:08,982] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:08,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:09,002] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:09,003] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:09,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015222005.1_ASM1522200v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:09,004] [INFO] Task started: Blastn
[2024-01-24 14:00:09,004] [INFO] Running command: blastn -query GCF_015222005.1_ASM1522200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg466137e8-b3c3-4ec7-83e2-88947d0cefaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_015222005.1_ASM1522200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:09,966] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:09,969] [INFO] Selected 19 target genomes.
[2024-01-24 14:00:09,970] [INFO] Target genome list was writen to GCF_015222005.1_ASM1522200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:10,000] [INFO] Task started: fastANI
[2024-01-24 14:00:10,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg4791de54-584f-4547-911b-4b722ebda85e/GCF_015222005.1_ASM1522200v1_genomic.fna.gz --refList GCF_015222005.1_ASM1522200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015222005.1_ASM1522200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:28,741] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:28,757] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:28,757] [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_015222005.1	s__Mucilaginibacter myungsuensis	100.0	1683	1683	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_013283875.1	s__Mucilaginibacter mali	78.0688	526	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221995.1	s__Mucilaginibacter boryungensis	77.9467	369	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050755.1	s__Mucilaginibacter yixingensis	77.5398	287	1683	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	77.5243	203	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928685.1	s__Mucilaginibacter sp009928685	77.4596	201	1683	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	77.383	227	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449775.1	s__Mucilaginibacter sp018449775	77.3366	198	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	77.3212	226	1683	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	77.1844	162	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200495.1	s__Mucilaginibacter sp014200495	77.1162	185	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773265.1	s__Mucilaginibacter pankratovii	77.0858	285	1683	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	77.02	227	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378255.1	s__Mucilaginibacter phyllosphaerae	76.993	240	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014205845.1	s__Mucilaginibacter sp014205845	76.9707	221	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	76.8457	241	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971525.1	s__Mucilaginibacter ginsenosidivorax	76.8106	237	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355435.1	s__Mucilaginibacter gotjawali	76.7212	169	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013286565.1	s__Mucilaginibacter sp013286565	76.5681	126	1683	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 14:00:28,761] [INFO] GTDB search result was written to GCF_015222005.1_ASM1522200v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:28,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:28,774] [INFO] DFAST_QC result json was written to GCF_015222005.1_ASM1522200v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:28,774] [INFO] DFAST_QC completed!
[2024-01-24 14:00:28,775] [INFO] Total running time: 0h2m18s