[2024-01-24 12:37:37,925] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,928] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,928] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfe28245-84ba-41c4-a5ca-ecb4a1e4e862/dqc_reference
[2024-01-24 12:37:41,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,021] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,021] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a2686b3-24a8-4b2d-a0c8-a800e01d5be2/GCF_025146135.1_ASM2514613v1_genomic.fna.gz | prodigal -d GCF_025146135.1_ASM2514613v1_genomic.fna/cds.fna -a GCF_025146135.1_ASM2514613v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:51,439] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:51,439] [INFO] Task started: HMMsearch
[2024-01-24 12:37:51,439] [INFO] Running command: hmmsearch --tblout GCF_025146135.1_ASM2514613v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfe28245-84ba-41c4-a5ca-ecb4a1e4e862/dqc_reference/reference_markers.hmm GCF_025146135.1_ASM2514613v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:51,693] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:51,695] [INFO] Found 6/6 markers.
[2024-01-24 12:37:51,734] [INFO] Query marker FASTA was written to GCF_025146135.1_ASM2514613v1_genomic.fna/markers.fasta
[2024-01-24 12:37:51,735] [INFO] Task started: Blastn
[2024-01-24 12:37:51,735] [INFO] Running command: blastn -query GCF_025146135.1_ASM2514613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfe28245-84ba-41c4-a5ca-ecb4a1e4e862/dqc_reference/reference_markers.fasta -out GCF_025146135.1_ASM2514613v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:52,421] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:52,424] [INFO] Selected 16 target genomes.
[2024-01-24 12:37:52,424] [INFO] Target genome list was writen to GCF_025146135.1_ASM2514613v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:52,434] [INFO] Task started: fastANI
[2024-01-24 12:37:52,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a2686b3-24a8-4b2d-a0c8-a800e01d5be2/GCF_025146135.1_ASM2514613v1_genomic.fna.gz --refList GCF_025146135.1_ASM2514613v1_genomic.fna/target_genomes.txt --output GCF_025146135.1_ASM2514613v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:04,043] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:04,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfe28245-84ba-41c4-a5ca-ecb4a1e4e862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:04,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfe28245-84ba-41c4-a5ca-ecb4a1e4e862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:04,052] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:38:04,052] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:04,053] [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
Anaerotruncus colihominis	strain=DSM 17241	GCA_025146135.1	169435	169435	type	True	100.0	1186	1187	95	conclusive
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	99.985	1166	1187	95	conclusive
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	78.606	233	1187	95	below_threshold
Marasmitruncus massiliensis	strain=Marseille-P3646	GCA_900186535.1	1944642	1944642	type	True	77.0224	100	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:04,054] [INFO] DFAST Taxonomy check result was written to GCF_025146135.1_ASM2514613v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:04,055] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:04,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:04,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfe28245-84ba-41c4-a5ca-ecb4a1e4e862/dqc_reference/checkm_data
[2024-01-24 12:38:04,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:04,098] [INFO] Task started: CheckM
[2024-01-24 12:38:04,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025146135.1_ASM2514613v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025146135.1_ASM2514613v1_genomic.fna/checkm_input GCF_025146135.1_ASM2514613v1_genomic.fna/checkm_result
[2024-01-24 12:38:38,816] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:38,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:38,836] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:38,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:38,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025146135.1_ASM2514613v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:38,837] [INFO] Task started: Blastn
[2024-01-24 12:38:38,837] [INFO] Running command: blastn -query GCF_025146135.1_ASM2514613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfe28245-84ba-41c4-a5ca-ecb4a1e4e862/dqc_reference/reference_markers_gtdb.fasta -out GCF_025146135.1_ASM2514613v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:39,954] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:39,958] [INFO] Selected 19 target genomes.
[2024-01-24 12:38:39,958] [INFO] Target genome list was writen to GCF_025146135.1_ASM2514613v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:40,003] [INFO] Task started: fastANI
[2024-01-24 12:38:40,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a2686b3-24a8-4b2d-a0c8-a800e01d5be2/GCF_025146135.1_ASM2514613v1_genomic.fna.gz --refList GCF_025146135.1_ASM2514613v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025146135.1_ASM2514613v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:49,423] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:49,433] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:49,434] [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_000154565.1	s__Anaerotruncus colihominis	99.985	1166	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.95	97.75	0.87	0.80	16	conclusive
GCF_010206195.1	s__Anaerotruncus colihominis_A	90.0493	805	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.98	98.75	0.89	0.87	3	-
GCA_014385085.1	s__Anaerotruncus sp014385085	80.7113	90	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014385025.1	s__Fimivivens sp014385025	80.4403	71	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fimivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199635.1	s__Anaerotruncus massiliensis	78.6052	232	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCF_000403395.2	s__Anaerotruncus sp000403395	78.3049	115	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.44	98.36	0.83	0.79	7	-
GCF_900078395.1	s__Anaerotruncus rubiinfantis	78.238	162	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.23	99.21	0.89	0.86	5	-
GCF_900186535.1	s__Anaerotruncus massiliensis_A	76.9989	101	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.01	98.01	0.87	0.87	2	-
GCA_019114825.1	s__Anaerotruncus excrementipullorum	76.8283	65	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.88	99.88	0.94	0.94	2	-
GCA_018716105.1	s__Fimivivens faecavium	76.5744	52	1187	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fimivivens	95.0	99.67	99.42	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:49,435] [INFO] GTDB search result was written to GCF_025146135.1_ASM2514613v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:49,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:49,441] [INFO] DFAST_QC result json was written to GCF_025146135.1_ASM2514613v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:49,441] [INFO] DFAST_QC completed!
[2024-01-24 12:38:49,441] [INFO] Total running time: 0h1m12s