[2024-01-24 11:34:55,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,234] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d6ecd78-f97c-423f-b56b-53bc1fd3bc11/dqc_reference
[2024-01-24 11:34:56,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,642] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,642] [INFO] Running command: gunzip -c /var/lib/cwl/stgc535365c-d200-4ea8-83b2-928ff0f96e10/GCF_016458825.1_ASM1645882v1_genomic.fna.gz | prodigal -d GCF_016458825.1_ASM1645882v1_genomic.fna/cds.fna -a GCF_016458825.1_ASM1645882v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:00,417] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:00,417] [INFO] Task started: HMMsearch
[2024-01-24 11:35:00,418] [INFO] Running command: hmmsearch --tblout GCF_016458825.1_ASM1645882v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d6ecd78-f97c-423f-b56b-53bc1fd3bc11/dqc_reference/reference_markers.hmm GCF_016458825.1_ASM1645882v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:00,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:00,703] [INFO] Found 6/6 markers.
[2024-01-24 11:35:00,726] [INFO] Query marker FASTA was written to GCF_016458825.1_ASM1645882v1_genomic.fna/markers.fasta
[2024-01-24 11:35:00,726] [INFO] Task started: Blastn
[2024-01-24 11:35:00,726] [INFO] Running command: blastn -query GCF_016458825.1_ASM1645882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d6ecd78-f97c-423f-b56b-53bc1fd3bc11/dqc_reference/reference_markers.fasta -out GCF_016458825.1_ASM1645882v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:01,604] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:01,609] [INFO] Selected 20 target genomes.
[2024-01-24 11:35:01,609] [INFO] Target genome list was writen to GCF_016458825.1_ASM1645882v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:01,744] [INFO] Task started: fastANI
[2024-01-24 11:35:01,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgc535365c-d200-4ea8-83b2-928ff0f96e10/GCF_016458825.1_ASM1645882v1_genomic.fna.gz --refList GCF_016458825.1_ASM1645882v1_genomic.fna/target_genomes.txt --output GCF_016458825.1_ASM1645882v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:10,146] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:10,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d6ecd78-f97c-423f-b56b-53bc1fd3bc11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:10,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d6ecd78-f97c-423f-b56b-53bc1fd3bc11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:10,155] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:10,155] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:10,155] [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
Miniphocaeibacter halophilus	strain=AMB_01	GCA_016458825.1	2931922	2931922	type	True	100.0	798	798	95	conclusive
Miniphocaeibacter massiliensis	strain=Marseille-P4678	GCA_900232905.1	2041841	2041841	type	True	78.199	254	798	95	below_threshold
Lagierella massiliensis	strain=Marseille-P2012	GCA_902375645.1	1689303	1689303	type	True	77.7103	75	798	95	below_threshold
Lagierella massiliensis	strain=SIT14	GCA_001407835.1	1689303	1689303	type	True	77.5167	73	798	95	below_threshold
Finegoldia magna	strain=FDAARGOS_1593	GCA_020731325.1	1260	1260	suspected-type	True	77.3691	50	798	95	below_threshold
Tissierella praeacuta	strain=DSM 18095	GCA_900128955.1	43131	43131	type	True	75.2661	53	798	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	74.9464	59	798	95	below_threshold
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	74.9084	54	798	95	below_threshold
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	74.7741	55	798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:10,157] [INFO] DFAST Taxonomy check result was written to GCF_016458825.1_ASM1645882v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:10,157] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:10,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:10,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d6ecd78-f97c-423f-b56b-53bc1fd3bc11/dqc_reference/checkm_data
[2024-01-24 11:35:10,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:10,193] [INFO] Task started: CheckM
[2024-01-24 11:35:10,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016458825.1_ASM1645882v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016458825.1_ASM1645882v1_genomic.fna/checkm_input GCF_016458825.1_ASM1645882v1_genomic.fna/checkm_result
[2024-01-24 11:35:29,321] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:29,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:29,343] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:29,343] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:29,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016458825.1_ASM1645882v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:29,344] [INFO] Task started: Blastn
[2024-01-24 11:35:29,344] [INFO] Running command: blastn -query GCF_016458825.1_ASM1645882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d6ecd78-f97c-423f-b56b-53bc1fd3bc11/dqc_reference/reference_markers_gtdb.fasta -out GCF_016458825.1_ASM1645882v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:30,238] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:30,242] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:30,242] [INFO] Target genome list was writen to GCF_016458825.1_ASM1645882v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:30,257] [INFO] Task started: fastANI
[2024-01-24 11:35:30,257] [INFO] Running command: fastANI --query /var/lib/cwl/stgc535365c-d200-4ea8-83b2-928ff0f96e10/GCF_016458825.1_ASM1645882v1_genomic.fna.gz --refList GCF_016458825.1_ASM1645882v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016458825.1_ASM1645882v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:37,112] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:37,125] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:37,125] [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_016458825.1	s__Miniphocibacter sp016458825	100.0	798	798	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Miniphocibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012841535.1	s__Miniphocibacter sp012841535	88.2396	550	798	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Miniphocibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900232905.1	s__Miniphocibacter massiliensis	78.199	254	798	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Miniphocibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001407835.1	s__Lagierella massiliensis	77.7103	75	798	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Lagierella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000214475.1	s__Parvimonas sp000214475	77.3034	66	798	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Parvimonas	95.0	97.82	97.68	0.91	0.90	3	-
GCA_001552895.1	s__Parvimonas sp001552895	76.6408	60	798	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Parvimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:37,127] [INFO] GTDB search result was written to GCF_016458825.1_ASM1645882v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:37,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:37,131] [INFO] DFAST_QC result json was written to GCF_016458825.1_ASM1645882v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:37,131] [INFO] DFAST_QC completed!
[2024-01-24 11:35:37,131] [INFO] Total running time: 0h0m42s