[2024-01-24 13:31:35,556] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,559] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdc8d50f-0f10-4c6b-9415-4434c7bbcac2/dqc_reference
[2024-01-24 13:31:36,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,987] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,987] [INFO] Running command: gunzip -c /var/lib/cwl/stg3290a43d-7da7-4359-8c09-15f4923671e4/GCF_014200545.1_ASM1420054v1_genomic.fna.gz | prodigal -d GCF_014200545.1_ASM1420054v1_genomic.fna/cds.fna -a GCF_014200545.1_ASM1420054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:06,065] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:06,066] [INFO] Task started: HMMsearch
[2024-01-24 13:32:06,066] [INFO] Running command: hmmsearch --tblout GCF_014200545.1_ASM1420054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdc8d50f-0f10-4c6b-9415-4434c7bbcac2/dqc_reference/reference_markers.hmm GCF_014200545.1_ASM1420054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:06,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:06,428] [INFO] Found 6/6 markers.
[2024-01-24 13:32:06,489] [INFO] Query marker FASTA was written to GCF_014200545.1_ASM1420054v1_genomic.fna/markers.fasta
[2024-01-24 13:32:06,490] [INFO] Task started: Blastn
[2024-01-24 13:32:06,490] [INFO] Running command: blastn -query GCF_014200545.1_ASM1420054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdc8d50f-0f10-4c6b-9415-4434c7bbcac2/dqc_reference/reference_markers.fasta -out GCF_014200545.1_ASM1420054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:07,106] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:07,109] [INFO] Selected 14 target genomes.
[2024-01-24 13:32:07,110] [INFO] Target genome list was writen to GCF_014200545.1_ASM1420054v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:07,117] [INFO] Task started: fastANI
[2024-01-24 13:32:07,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg3290a43d-7da7-4359-8c09-15f4923671e4/GCF_014200545.1_ASM1420054v1_genomic.fna.gz --refList GCF_014200545.1_ASM1420054v1_genomic.fna/target_genomes.txt --output GCF_014200545.1_ASM1420054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:25,883] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:25,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdc8d50f-0f10-4c6b-9415-4434c7bbcac2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:25,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdc8d50f-0f10-4c6b-9415-4434c7bbcac2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:25,899] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:25,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:25,899] [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 lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	100.0	2236	2239	95	conclusive
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	99.9987	2236	2239	95	conclusive
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	88.3023	1807	2239	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	79.3994	790	2239	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	79.1154	753	2239	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	78.5804	713	2239	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	78.5219	703	2239	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	78.5162	711	2239	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	78.3813	716	2239	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.3768	260	2239	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.3154	333	2239	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.302	277	2239	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.2937	286	2239	95	below_threshold
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	76.505	57	2239	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:25,901] [INFO] DFAST Taxonomy check result was written to GCF_014200545.1_ASM1420054v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:25,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:25,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:25,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdc8d50f-0f10-4c6b-9415-4434c7bbcac2/dqc_reference/checkm_data
[2024-01-24 13:32:25,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:25,967] [INFO] Task started: CheckM
[2024-01-24 13:32:25,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014200545.1_ASM1420054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014200545.1_ASM1420054v1_genomic.fna/checkm_input GCF_014200545.1_ASM1420054v1_genomic.fna/checkm_result
[2024-01-24 13:33:46,351] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:46,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:46,377] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:46,377] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:46,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014200545.1_ASM1420054v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:46,378] [INFO] Task started: Blastn
[2024-01-24 13:33:46,378] [INFO] Running command: blastn -query GCF_014200545.1_ASM1420054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdc8d50f-0f10-4c6b-9415-4434c7bbcac2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014200545.1_ASM1420054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:47,162] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:47,166] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:47,166] [INFO] Target genome list was writen to GCF_014200545.1_ASM1420054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:47,185] [INFO] Task started: fastANI
[2024-01-24 13:33:47,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg3290a43d-7da7-4359-8c09-15f4923671e4/GCF_014200545.1_ASM1420054v1_genomic.fna.gz --refList GCF_014200545.1_ASM1420054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014200545.1_ASM1420054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:00,740] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:00,752] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:00,752] [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_900155965.1	s__Mucilaginibacter lappiensis	99.9987	2236	2239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.12	98.24	0.94	0.88	3	conclusive
GCF_011089895.1	s__Mucilaginibacter inviolabilis	88.3023	1807	2239	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	87.2565	1652	2239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149275.1	s__Mucilaginibacter sp013149275	85.3884	1613	2239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200575.1	s__Mucilaginibacter sp014200575	80.5014	1026	2239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101875.1	s__Mucilaginibacter pineti	79.4132	787	2239	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	79.3786	798	2239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100945.1	s__Mucilaginibacter gossypii	78.3952	714	2239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	96.19	95.83	0.85	0.84	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:00,755] [INFO] GTDB search result was written to GCF_014200545.1_ASM1420054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:00,755] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:00,759] [INFO] DFAST_QC result json was written to GCF_014200545.1_ASM1420054v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:00,759] [INFO] DFAST_QC completed!
[2024-01-24 13:34:00,759] [INFO] Total running time: 0h2m25s