[2024-01-24 13:51:12,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:12,158] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:12,158] [INFO] DQC Reference Directory: /var/lib/cwl/stgff082ebe-c9a0-4511-8ee2-c0e003246014/dqc_reference
[2024-01-24 13:51:13,365] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:13,367] [INFO] Task started: Prodigal
[2024-01-24 13:51:13,368] [INFO] Running command: gunzip -c /var/lib/cwl/stg2487a05d-ac0e-4f3f-b519-ccf63939241a/GCF_030273445.1_ASM3027344v1_genomic.fna.gz | prodigal -d GCF_030273445.1_ASM3027344v1_genomic.fna/cds.fna -a GCF_030273445.1_ASM3027344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:18,762] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:18,763] [INFO] Task started: HMMsearch
[2024-01-24 13:51:18,763] [INFO] Running command: hmmsearch --tblout GCF_030273445.1_ASM3027344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff082ebe-c9a0-4511-8ee2-c0e003246014/dqc_reference/reference_markers.hmm GCF_030273445.1_ASM3027344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:19,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:19,025] [INFO] Found 6/6 markers.
[2024-01-24 13:51:19,058] [INFO] Query marker FASTA was written to GCF_030273445.1_ASM3027344v1_genomic.fna/markers.fasta
[2024-01-24 13:51:19,058] [INFO] Task started: Blastn
[2024-01-24 13:51:19,059] [INFO] Running command: blastn -query GCF_030273445.1_ASM3027344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff082ebe-c9a0-4511-8ee2-c0e003246014/dqc_reference/reference_markers.fasta -out GCF_030273445.1_ASM3027344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:19,701] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:19,705] [INFO] Selected 16 target genomes.
[2024-01-24 13:51:19,706] [INFO] Target genome list was writen to GCF_030273445.1_ASM3027344v1_genomic.fna/target_genomes.txt
[2024-01-24 13:51:19,718] [INFO] Task started: fastANI
[2024-01-24 13:51:19,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg2487a05d-ac0e-4f3f-b519-ccf63939241a/GCF_030273445.1_ASM3027344v1_genomic.fna.gz --refList GCF_030273445.1_ASM3027344v1_genomic.fna/target_genomes.txt --output GCF_030273445.1_ASM3027344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:27,878] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:27,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff082ebe-c9a0-4511-8ee2-c0e003246014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:27,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff082ebe-c9a0-4511-8ee2-c0e003246014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:27,889] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:51:27,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:51:27,890] [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
Megamonas funiformis	strain=JCM 14723	GCA_010669225.1	437897	437897	type	True	78.8654	69	893	95	below_threshold
Massilibacillus massiliensis	strain=Marseille-P2411	GCA_900086705.1	1806837	1806837	type	True	78.5288	177	893	95	below_threshold
Megamonas funiformis	strain=YIT 11815	GCA_000245775.1	437897	437897	type	True	78.4789	64	893	95	below_threshold
Propionispira arboris	strain=DSM 2179	GCA_900109225.1	84035	84035	type	True	77.6239	96	893	95	below_threshold
Propionispira raffinosivorans	strain=DSM 20765	GCA_000381065.1	86959	86959	type	True	77.5797	96	893	95	below_threshold
Pelosinus propionicus	strain=DSM 13327	GCA_900114615.1	380084	380084	type	True	77.0492	60	893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:27,892] [INFO] DFAST Taxonomy check result was written to GCF_030273445.1_ASM3027344v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:27,893] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:27,893] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:27,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff082ebe-c9a0-4511-8ee2-c0e003246014/dqc_reference/checkm_data
[2024-01-24 13:51:27,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:27,927] [INFO] Task started: CheckM
[2024-01-24 13:51:27,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030273445.1_ASM3027344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030273445.1_ASM3027344v1_genomic.fna/checkm_input GCF_030273445.1_ASM3027344v1_genomic.fna/checkm_result
[2024-01-24 13:51:51,209] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:51,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:51,233] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:51,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:51,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030273445.1_ASM3027344v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:51,234] [INFO] Task started: Blastn
[2024-01-24 13:51:51,234] [INFO] Running command: blastn -query GCF_030273445.1_ASM3027344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff082ebe-c9a0-4511-8ee2-c0e003246014/dqc_reference/reference_markers_gtdb.fasta -out GCF_030273445.1_ASM3027344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:52,084] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:52,088] [INFO] Selected 14 target genomes.
[2024-01-24 13:51:52,088] [INFO] Target genome list was writen to GCF_030273445.1_ASM3027344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:52,099] [INFO] Task started: fastANI
[2024-01-24 13:51:52,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg2487a05d-ac0e-4f3f-b519-ccf63939241a/GCF_030273445.1_ASM3027344v1_genomic.fna.gz --refList GCF_030273445.1_ASM3027344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030273445.1_ASM3027344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:58,903] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:58,915] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:58,915] [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_902363205.1	s__CABIZH01 sp902363205	99.9462	851	893	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Massilibacillaceae;g__CABIZH01	95.0	97.61	97.54	0.87	0.81	4	conclusive
GCF_010669225.1	s__Megamonas funiformis	79.2359	68	893	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	97.89	97.23	0.89	0.80	26	-
GCF_900086705.1	s__Massilibacillus massiliensis	78.7439	178	893	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Massilibacillaceae;g__Massilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018052945.1	s__JAGPMH01 sp018052945	77.6573	103	893	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__JAGPMH01;g__JAGPMH01	95.0	99.69	99.53	0.94	0.93	4	-
GCF_900109225.1	s__Propionispira arboris	77.6324	95	893	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira	96.4486	N/A	N/A	N/A	N/A	1	-
GCF_000381065.1	s__Propionispira raffinosivorans	77.5805	96	893	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira	96.4486	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:58,917] [INFO] GTDB search result was written to GCF_030273445.1_ASM3027344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:58,917] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:58,921] [INFO] DFAST_QC result json was written to GCF_030273445.1_ASM3027344v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:58,921] [INFO] DFAST_QC completed!
[2024-01-24 13:51:58,922] [INFO] Total running time: 0h0m47s