[2024-01-24 11:52:04,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgee20e33e-9156-4e99-8998-14588f4e906c/dqc_reference
[2024-01-24 11:52:05,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:05,987] [INFO] Task started: Prodigal
[2024-01-24 11:52:05,988] [INFO] Running command: gunzip -c /var/lib/cwl/stga9c3d823-f68d-4193-8852-c7aa69d451e2/GCF_024622025.1_ASM2462202v1_genomic.fna.gz | prodigal -d GCF_024622025.1_ASM2462202v1_genomic.fna/cds.fna -a GCF_024622025.1_ASM2462202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:33,643] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:33,644] [INFO] Task started: HMMsearch
[2024-01-24 11:52:33,644] [INFO] Running command: hmmsearch --tblout GCF_024622025.1_ASM2462202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee20e33e-9156-4e99-8998-14588f4e906c/dqc_reference/reference_markers.hmm GCF_024622025.1_ASM2462202v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:33,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:33,931] [INFO] Found 6/6 markers.
[2024-01-24 11:52:33,976] [INFO] Query marker FASTA was written to GCF_024622025.1_ASM2462202v1_genomic.fna/markers.fasta
[2024-01-24 11:52:33,977] [INFO] Task started: Blastn
[2024-01-24 11:52:33,977] [INFO] Running command: blastn -query GCF_024622025.1_ASM2462202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee20e33e-9156-4e99-8998-14588f4e906c/dqc_reference/reference_markers.fasta -out GCF_024622025.1_ASM2462202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:34,575] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:34,580] [INFO] Selected 10 target genomes.
[2024-01-24 11:52:34,581] [INFO] Target genome list was writen to GCF_024622025.1_ASM2462202v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:34,590] [INFO] Task started: fastANI
[2024-01-24 11:52:34,590] [INFO] Running command: fastANI --query /var/lib/cwl/stga9c3d823-f68d-4193-8852-c7aa69d451e2/GCF_024622025.1_ASM2462202v1_genomic.fna.gz --refList GCF_024622025.1_ASM2462202v1_genomic.fna/target_genomes.txt --output GCF_024622025.1_ASM2462202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:44,729] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:44,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee20e33e-9156-4e99-8998-14588f4e906c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:44,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee20e33e-9156-4e99-8998-14588f4e906c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:44,740] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:44,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:44,740] [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
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	100.0	1718	1720	95	conclusive
Phocaeicola sartorii	strain=JCM 17136	GCA_000614185.1	671267	671267	type	True	99.9252	1657	1720	95	conclusive
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	90.1862	1105	1720	95	below_threshold
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	90.1275	1101	1720	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_000156075.1	357276	357276	type	True	89.8952	1137	1720	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	89.8866	1156	1720	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	89.8566	1143	1720	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	80.6768	592	1720	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	79.7829	215	1720	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	78.1575	200	1720	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:44,742] [INFO] DFAST Taxonomy check result was written to GCF_024622025.1_ASM2462202v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:44,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:44,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:44,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee20e33e-9156-4e99-8998-14588f4e906c/dqc_reference/checkm_data
[2024-01-24 11:52:44,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:44,793] [INFO] Task started: CheckM
[2024-01-24 11:52:44,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024622025.1_ASM2462202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024622025.1_ASM2462202v1_genomic.fna/checkm_input GCF_024622025.1_ASM2462202v1_genomic.fna/checkm_result
[2024-01-24 11:54:01,021] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:01,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:01,049] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:01,049] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:01,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024622025.1_ASM2462202v1_genomic.fna/markers.fasta)
[2024-01-24 11:54:01,050] [INFO] Task started: Blastn
[2024-01-24 11:54:01,050] [INFO] Running command: blastn -query GCF_024622025.1_ASM2462202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee20e33e-9156-4e99-8998-14588f4e906c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024622025.1_ASM2462202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:01,871] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:01,875] [INFO] Selected 6 target genomes.
[2024-01-24 11:54:01,875] [INFO] Target genome list was writen to GCF_024622025.1_ASM2462202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:01,882] [INFO] Task started: fastANI
[2024-01-24 11:54:01,883] [INFO] Running command: fastANI --query /var/lib/cwl/stga9c3d823-f68d-4193-8852-c7aa69d451e2/GCF_024622025.1_ASM2462202v1_genomic.fna.gz --refList GCF_024622025.1_ASM2462202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024622025.1_ASM2462202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:08,590] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:08,599] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:08,599] [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_000614185.1	s__Phocaeicola sartorii	99.9252	1657	1720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.95	98.44	0.85	0.76	7	conclusive
GCA_011959205.1	s__Phocaeicola sp011959205	92.6277	886	1720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.90	0.90	2	-
GCF_000012825.1	s__Phocaeicola vulgatus	90.1318	1101	1720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	98.84	95.43	0.81	0.61	263	-
GCF_013009555.1	s__Phocaeicola dorei	89.8685	1142	1720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	99.04	97.27	0.84	0.54	104	-
GCA_900760795.1	s__Phocaeicola sp900760795	86.6195	700	1720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902388365.1	s__Phocaeicola sp902388365	81.1849	818	1720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.75	97.52	0.90	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:08,601] [INFO] GTDB search result was written to GCF_024622025.1_ASM2462202v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:08,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:08,608] [INFO] DFAST_QC result json was written to GCF_024622025.1_ASM2462202v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:08,608] [INFO] DFAST_QC completed!
[2024-01-24 11:54:08,608] [INFO] Total running time: 0h2m4s