[2024-01-24 14:22:17,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,504] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc75cceb-da51-47b2-aaa9-aa04d2eac826/dqc_reference
[2024-01-24 14:22:18,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,774] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,775] [INFO] Running command: gunzip -c /var/lib/cwl/stgd087b0e0-42d6-4e90-a8b1-7a3cf99e5a69/GCF_025566985.1_ASM2556698v1_genomic.fna.gz | prodigal -d GCF_025566985.1_ASM2556698v1_genomic.fna/cds.fna -a GCF_025566985.1_ASM2556698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:23,961] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:23,962] [INFO] Task started: HMMsearch
[2024-01-24 14:22:23,962] [INFO] Running command: hmmsearch --tblout GCF_025566985.1_ASM2556698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc75cceb-da51-47b2-aaa9-aa04d2eac826/dqc_reference/reference_markers.hmm GCF_025566985.1_ASM2556698v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:24,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:24,189] [INFO] Found 6/6 markers.
[2024-01-24 14:22:24,212] [INFO] Query marker FASTA was written to GCF_025566985.1_ASM2556698v1_genomic.fna/markers.fasta
[2024-01-24 14:22:24,212] [INFO] Task started: Blastn
[2024-01-24 14:22:24,212] [INFO] Running command: blastn -query GCF_025566985.1_ASM2556698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc75cceb-da51-47b2-aaa9-aa04d2eac826/dqc_reference/reference_markers.fasta -out GCF_025566985.1_ASM2556698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:24,817] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:24,822] [INFO] Selected 10 target genomes.
[2024-01-24 14:22:24,822] [INFO] Target genome list was writen to GCF_025566985.1_ASM2556698v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:24,839] [INFO] Task started: fastANI
[2024-01-24 14:22:24,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgd087b0e0-42d6-4e90-a8b1-7a3cf99e5a69/GCF_025566985.1_ASM2556698v1_genomic.fna.gz --refList GCF_025566985.1_ASM2556698v1_genomic.fna/target_genomes.txt --output GCF_025566985.1_ASM2556698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:29,567] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:29,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc75cceb-da51-47b2-aaa9-aa04d2eac826/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:29,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc75cceb-da51-47b2-aaa9-aa04d2eac826/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:29,578] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:29,579] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:29,579] [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
Peptoniphilus rachelemmaiella	strain=EMRHCC_23	GCA_943169845.1	2811779	2811779	type	True	89.5314	502	637	95	below_threshold
Peptoniphilus pacaensis	strain=Kh-D5	GCA_900088125.1	1776390	1776390	type	True	86.2612	477	637	95	below_threshold
Peptoniphilus urinimassiliensis	strain=Marseille-P3195	GCA_900155585.1	1871017	1871017	type	True	85.8571	465	637	95	below_threshold
Peptoniphilus nemausensis	strain=1804121828	GCA_903819165.1	2582829	2582829	type	True	80.7614	262	637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:29,581] [INFO] DFAST Taxonomy check result was written to GCF_025566985.1_ASM2556698v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:29,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:29,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:29,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc75cceb-da51-47b2-aaa9-aa04d2eac826/dqc_reference/checkm_data
[2024-01-24 14:22:29,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:29,608] [INFO] Task started: CheckM
[2024-01-24 14:22:29,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025566985.1_ASM2556698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025566985.1_ASM2556698v1_genomic.fna/checkm_input GCF_025566985.1_ASM2556698v1_genomic.fna/checkm_result
[2024-01-24 14:22:51,592] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:51,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:51,613] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:51,613] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:51,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025566985.1_ASM2556698v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:51,614] [INFO] Task started: Blastn
[2024-01-24 14:22:51,614] [INFO] Running command: blastn -query GCF_025566985.1_ASM2556698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc75cceb-da51-47b2-aaa9-aa04d2eac826/dqc_reference/reference_markers_gtdb.fasta -out GCF_025566985.1_ASM2556698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:52,479] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:52,483] [INFO] Selected 9 target genomes.
[2024-01-24 14:22:52,484] [INFO] Target genome list was writen to GCF_025566985.1_ASM2556698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:52,503] [INFO] Task started: fastANI
[2024-01-24 14:22:52,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgd087b0e0-42d6-4e90-a8b1-7a3cf99e5a69/GCF_025566985.1_ASM2556698v1_genomic.fna.gz --refList GCF_025566985.1_ASM2556698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025566985.1_ASM2556698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:56,576] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:56,590] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:56,591] [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
GCA_902363535.1	s__Peptoniphilus_C sp902363535	100.0	634	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	97.41	97.41	0.94	0.94	2	conclusive
GCF_900343085.1	s__Peptoniphilus_C sp900343085	94.635	537	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900088125.1	s__Peptoniphilus_C pacaensis	86.2736	477	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155585.1	s__Peptoniphilus_C urinimassiliensis	85.8357	466	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553115.1	s__Peptoniphilus_C coxii	81.3382	294	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903819165.1	s__Peptoniphilus_C nemausensis	80.7313	264	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900638585.1	s__Peptoniphilus_C ivorii	78.436	187	637	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:56,594] [INFO] GTDB search result was written to GCF_025566985.1_ASM2556698v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:56,595] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:56,598] [INFO] DFAST_QC result json was written to GCF_025566985.1_ASM2556698v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:56,598] [INFO] DFAST_QC completed!
[2024-01-24 14:22:56,598] [INFO] Total running time: 0h0m39s