[2024-01-24 13:18:27,701] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,703] [INFO] DQC Reference Directory: /var/lib/cwl/stgf81878fd-f4b3-42c3-89f6-5cd2b1465d92/dqc_reference
[2024-01-24 13:18:29,028] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:29,029] [INFO] Task started: Prodigal
[2024-01-24 13:18:29,029] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb7dff5e-7a62-40e2-9fd7-15848a95539f/GCF_031202285.1_ASM3120228v1_genomic.fna.gz | prodigal -d GCF_031202285.1_ASM3120228v1_genomic.fna/cds.fna -a GCF_031202285.1_ASM3120228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:35,783] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:35,784] [INFO] Task started: HMMsearch
[2024-01-24 13:18:35,784] [INFO] Running command: hmmsearch --tblout GCF_031202285.1_ASM3120228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf81878fd-f4b3-42c3-89f6-5cd2b1465d92/dqc_reference/reference_markers.hmm GCF_031202285.1_ASM3120228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:36,131] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:36,133] [INFO] Found 6/6 markers.
[2024-01-24 13:18:36,168] [INFO] Query marker FASTA was written to GCF_031202285.1_ASM3120228v1_genomic.fna/markers.fasta
[2024-01-24 13:18:36,169] [INFO] Task started: Blastn
[2024-01-24 13:18:36,169] [INFO] Running command: blastn -query GCF_031202285.1_ASM3120228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf81878fd-f4b3-42c3-89f6-5cd2b1465d92/dqc_reference/reference_markers.fasta -out GCF_031202285.1_ASM3120228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:37,102] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:37,105] [INFO] Selected 5 target genomes.
[2024-01-24 13:18:37,105] [INFO] Target genome list was writen to GCF_031202285.1_ASM3120228v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:37,110] [INFO] Task started: fastANI
[2024-01-24 13:18:37,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7dff5e-7a62-40e2-9fd7-15848a95539f/GCF_031202285.1_ASM3120228v1_genomic.fna.gz --refList GCF_031202285.1_ASM3120228v1_genomic.fna/target_genomes.txt --output GCF_031202285.1_ASM3120228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:42,719] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:42,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf81878fd-f4b3-42c3-89f6-5cd2b1465d92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:42,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf81878fd-f4b3-42c3-89f6-5cd2b1465d92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:42,734] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:42,734] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:42,734] [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
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	99.978	1323	1353	95	conclusive
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	93.0471	1110	1353	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	93.047	1120	1353	95	below_threshold
Terrisporobacter petrolearius	strain=LAM0A37	GCA_020748185.1	1460447	1460447	type	True	91.7323	1065	1353	95	below_threshold
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	87.3156	919	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:42,736] [INFO] DFAST Taxonomy check result was written to GCF_031202285.1_ASM3120228v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:42,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:42,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:42,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf81878fd-f4b3-42c3-89f6-5cd2b1465d92/dqc_reference/checkm_data
[2024-01-24 13:18:42,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:42,778] [INFO] Task started: CheckM
[2024-01-24 13:18:42,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031202285.1_ASM3120228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031202285.1_ASM3120228v1_genomic.fna/checkm_input GCF_031202285.1_ASM3120228v1_genomic.fna/checkm_result
[2024-01-24 13:19:08,842] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:08,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:08,867] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:08,868] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:08,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031202285.1_ASM3120228v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:08,869] [INFO] Task started: Blastn
[2024-01-24 13:19:08,869] [INFO] Running command: blastn -query GCF_031202285.1_ASM3120228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf81878fd-f4b3-42c3-89f6-5cd2b1465d92/dqc_reference/reference_markers_gtdb.fasta -out GCF_031202285.1_ASM3120228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:09,670] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:09,673] [INFO] Selected 6 target genomes.
[2024-01-24 13:19:09,673] [INFO] Target genome list was writen to GCF_031202285.1_ASM3120228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:09,678] [INFO] Task started: fastANI
[2024-01-24 13:19:09,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7dff5e-7a62-40e2-9fd7-15848a95539f/GCF_031202285.1_ASM3120228v1_genomic.fna.gz --refList GCF_031202285.1_ASM3120228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031202285.1_ASM3120228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:15,518] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:15,529] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:19:15,529] [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_000439105.1	s__Terrisporobacter glycolicus	93.047	1120	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.67	99.35	0.98	0.96	3	-
GCF_900114105.1	s__Terrisporobacter glycolicus_A	91.692	1101	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	98.29	98.07	0.91	0.91	3	-
GCF_000808015.1	s__Terrisporobacter othiniensis	87.3296	918	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.48	99.45	0.91	0.90	3	-
GCA_902363255.1	s__Terrisporobacter sp902363255	86.3791	888	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333445.1	s__Terrisporobacter mayombei	83.11	307	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557165.1	s__Terrisporobacter sp900557165	82.4276	474	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.06	99.06	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:15,531] [INFO] GTDB search result was written to GCF_031202285.1_ASM3120228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:15,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:15,535] [INFO] DFAST_QC result json was written to GCF_031202285.1_ASM3120228v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:15,535] [INFO] DFAST_QC completed!
[2024-01-24 13:19:15,535] [INFO] Total running time: 0h0m48s