[2023-06-27 04:40:56,461] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:40:56,468] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:40:56,468] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa71379f-6159-45df-840e-e296aca79344/dqc_reference
[2023-06-27 04:40:57,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:40:57,951] [INFO] Task started: Prodigal
[2023-06-27 04:40:57,952] [INFO] Running command: gunzip -c /var/lib/cwl/stga7e7e21e-ffb7-4846-b92d-686942ffcd48/GCA_026645875.1_ASM2664587v1_genomic.fna.gz | prodigal -d GCA_026645875.1_ASM2664587v1_genomic.fna/cds.fna -a GCA_026645875.1_ASM2664587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:41:06,135] [INFO] Task succeeded: Prodigal
[2023-06-27 04:41:06,135] [INFO] Task started: HMMsearch
[2023-06-27 04:41:06,135] [INFO] Running command: hmmsearch --tblout GCA_026645875.1_ASM2664587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa71379f-6159-45df-840e-e296aca79344/dqc_reference/reference_markers.hmm GCA_026645875.1_ASM2664587v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:41:06,413] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:41:06,414] [INFO] Found 6/6 markers.
[2023-06-27 04:41:06,460] [INFO] Query marker FASTA was written to GCA_026645875.1_ASM2664587v1_genomic.fna/markers.fasta
[2023-06-27 04:41:06,461] [INFO] Task started: Blastn
[2023-06-27 04:41:06,461] [INFO] Running command: blastn -query GCA_026645875.1_ASM2664587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa71379f-6159-45df-840e-e296aca79344/dqc_reference/reference_markers.fasta -out GCA_026645875.1_ASM2664587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:41:07,135] [INFO] Task succeeded: Blastn
[2023-06-27 04:41:07,152] [INFO] Selected 21 target genomes.
[2023-06-27 04:41:07,152] [INFO] Target genome list was writen to GCA_026645875.1_ASM2664587v1_genomic.fna/target_genomes.txt
[2023-06-27 04:41:07,157] [INFO] Task started: fastANI
[2023-06-27 04:41:07,157] [INFO] Running command: fastANI --query /var/lib/cwl/stga7e7e21e-ffb7-4846-b92d-686942ffcd48/GCA_026645875.1_ASM2664587v1_genomic.fna.gz --refList GCA_026645875.1_ASM2664587v1_genomic.fna/target_genomes.txt --output GCA_026645875.1_ASM2664587v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 04:41:22,658] [INFO] Task succeeded: fastANI
[2023-06-27 04:41:22,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa71379f-6159-45df-840e-e296aca79344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 04:41:22,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa71379f-6159-45df-840e-e296aca79344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 04:41:22,665] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 04:41:22,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 04:41:22,666] [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
Longilinea arvoryzae	strain=KOME-1	GCA_001050235.2	360412	360412	type	True	79.365	390	815	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001050255.2	229921	229921	type	True	77.0266	112	815	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001306035.1	229921	229921	type	True	76.9871	114	815	95	below_threshold
Ornatilinea apprima	strain=P3M-1	GCA_001306115.1	1134406	1134406	type	True	76.3714	72	815	95	below_threshold
Anaerolinea thermophila	strain=UNI-1	GCA_000199675.1	167964	167964	type	True	75.959	53	815	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 04:41:22,675] [INFO] DFAST Taxonomy check result was written to GCA_026645875.1_ASM2664587v1_genomic.fna/tc_result.tsv
[2023-06-27 04:41:22,675] [INFO] ===== Taxonomy check completed =====
[2023-06-27 04:41:22,676] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 04:41:22,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa71379f-6159-45df-840e-e296aca79344/dqc_reference/checkm_data
[2023-06-27 04:41:22,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 04:41:22,713] [INFO] Task started: CheckM
[2023-06-27 04:41:22,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026645875.1_ASM2664587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026645875.1_ASM2664587v1_genomic.fna/checkm_input GCA_026645875.1_ASM2664587v1_genomic.fna/checkm_result
[2023-06-27 04:41:51,965] [INFO] Task succeeded: CheckM
[2023-06-27 04:41:51,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 04:41:51,991] [INFO] ===== Completeness check finished =====
[2023-06-27 04:41:51,992] [INFO] ===== Start GTDB Search =====
[2023-06-27 04:41:51,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026645875.1_ASM2664587v1_genomic.fna/markers.fasta)
[2023-06-27 04:41:51,992] [INFO] Task started: Blastn
[2023-06-27 04:41:51,993] [INFO] Running command: blastn -query GCA_026645875.1_ASM2664587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa71379f-6159-45df-840e-e296aca79344/dqc_reference/reference_markers_gtdb.fasta -out GCA_026645875.1_ASM2664587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:41:52,789] [INFO] Task succeeded: Blastn
[2023-06-27 04:41:52,794] [INFO] Selected 28 target genomes.
[2023-06-27 04:41:52,794] [INFO] Target genome list was writen to GCA_026645875.1_ASM2664587v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 04:41:52,817] [INFO] Task started: fastANI
[2023-06-27 04:41:52,817] [INFO] Running command: fastANI --query /var/lib/cwl/stga7e7e21e-ffb7-4846-b92d-686942ffcd48/GCA_026645875.1_ASM2664587v1_genomic.fna.gz --refList GCA_026645875.1_ASM2664587v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026645875.1_ASM2664587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 04:42:08,421] [INFO] Task succeeded: fastANI
[2023-06-27 04:42:08,434] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 04:42:08,435] [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_001050235.1	s__Longilinea arvoryzae	79.3523	391	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Longilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306035.1	s__Levilinea saccharolytica	76.9871	114	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Levilinea	95.0	99.90	99.90	0.95	0.95	2	-
GCA_002385985.1	s__UBA3924 sp002385985	76.8169	99	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA3924	95.0	99.86	99.86	0.92	0.92	2	-
GCA_002298885.1	s__UBA700 sp002298885	76.4284	74	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA700	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306115.1	s__Ornatilinea apprima	76.3674	72	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Ornatilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772985.1	s__UBA877 sp009772985	76.2999	69	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798515.1	s__JAAZNB01 sp012798515	76.1004	81	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__JAAZNB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016927865.1	s__Anaerolinea sp016927865	76.0933	99	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191875.1	s__SCUK01 sp016191875	76.0718	54	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11579;g__SCUK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428565.1	s__UBA6092 sp002428565	75.9668	93	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__UBA6092	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000199675.1	s__Anaerolinea thermophila	75.959	53	815	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 04:42:08,438] [INFO] GTDB search result was written to GCA_026645875.1_ASM2664587v1_genomic.fna/result_gtdb.tsv
[2023-06-27 04:42:08,438] [INFO] ===== GTDB Search completed =====
[2023-06-27 04:42:08,443] [INFO] DFAST_QC result json was written to GCA_026645875.1_ASM2664587v1_genomic.fna/dqc_result.json
[2023-06-27 04:42:08,443] [INFO] DFAST_QC completed!
[2023-06-27 04:42:08,443] [INFO] Total running time: 0h1m12s