[2024-01-24 15:27:21,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:21,296] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:21,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg798ad0ce-ca68-4f71-babc-ab466f6d450b/dqc_reference
[2024-01-24 15:27:22,652] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:22,652] [INFO] Task started: Prodigal
[2024-01-24 15:27:22,653] [INFO] Running command: gunzip -c /var/lib/cwl/stgf68ee04a-7fcd-44f8-a82c-c7a8de0dc305/GCF_016820635.1_ASM1682063v1_genomic.fna.gz | prodigal -d GCF_016820635.1_ASM1682063v1_genomic.fna/cds.fna -a GCF_016820635.1_ASM1682063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:26,851] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:26,852] [INFO] Task started: HMMsearch
[2024-01-24 15:27:26,852] [INFO] Running command: hmmsearch --tblout GCF_016820635.1_ASM1682063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg798ad0ce-ca68-4f71-babc-ab466f6d450b/dqc_reference/reference_markers.hmm GCF_016820635.1_ASM1682063v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:27,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:27,117] [INFO] Found 6/6 markers.
[2024-01-24 15:27:27,143] [INFO] Query marker FASTA was written to GCF_016820635.1_ASM1682063v1_genomic.fna/markers.fasta
[2024-01-24 15:27:27,143] [INFO] Task started: Blastn
[2024-01-24 15:27:27,143] [INFO] Running command: blastn -query GCF_016820635.1_ASM1682063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg798ad0ce-ca68-4f71-babc-ab466f6d450b/dqc_reference/reference_markers.fasta -out GCF_016820635.1_ASM1682063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:27,857] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:27,860] [INFO] Selected 18 target genomes.
[2024-01-24 15:27:27,860] [INFO] Target genome list was writen to GCF_016820635.1_ASM1682063v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:27,875] [INFO] Task started: fastANI
[2024-01-24 15:27:27,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgf68ee04a-7fcd-44f8-a82c-c7a8de0dc305/GCF_016820635.1_ASM1682063v1_genomic.fna.gz --refList GCF_016820635.1_ASM1682063v1_genomic.fna/target_genomes.txt --output GCF_016820635.1_ASM1682063v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:38,066] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:38,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg798ad0ce-ca68-4f71-babc-ab466f6d450b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:38,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg798ad0ce-ca68-4f71-babc-ab466f6d450b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:38,081] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:38,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:38,081] [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
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	100.0	884	887	95	conclusive
Anaeromonas frigoriresistens	strain=D2Q-11	GCA_016820655.1	2683708	2683708	type	True	79.6946	439	887	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	78.2647	323	887	95	below_threshold
Clostridiisalibacter paucivorans	strain=DSM 22131	GCA_000620125.1	408753	408753	type	True	76.8686	114	887	95	below_threshold
Caldisalinibacter kiritimatiensis	strain=L21-TH-D2	GCA_000387765.1	1304284	1304284	type	True	76.2004	100	887	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	76.1592	115	887	95	below_threshold
Thermohalobacter berrensis	strain=CTT3	GCA_003609645.1	99594	99594	type	True	76.1178	111	887	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	75.8804	98	887	95	below_threshold
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	75.758	84	887	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	75.6782	88	887	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	75.6271	101	887	95	below_threshold
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	75.5875	72	887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:38,083] [INFO] DFAST Taxonomy check result was written to GCF_016820635.1_ASM1682063v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:38,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:38,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:38,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg798ad0ce-ca68-4f71-babc-ab466f6d450b/dqc_reference/checkm_data
[2024-01-24 15:27:38,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:38,117] [INFO] Task started: CheckM
[2024-01-24 15:27:38,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016820635.1_ASM1682063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016820635.1_ASM1682063v1_genomic.fna/checkm_input GCF_016820635.1_ASM1682063v1_genomic.fna/checkm_result
[2024-01-24 15:27:59,250] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:59,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:59,270] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:59,270] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:59,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016820635.1_ASM1682063v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:59,271] [INFO] Task started: Blastn
[2024-01-24 15:27:59,271] [INFO] Running command: blastn -query GCF_016820635.1_ASM1682063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg798ad0ce-ca68-4f71-babc-ab466f6d450b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016820635.1_ASM1682063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:00,111] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:00,114] [INFO] Selected 20 target genomes.
[2024-01-24 15:28:00,115] [INFO] Target genome list was writen to GCF_016820635.1_ASM1682063v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:00,132] [INFO] Task started: fastANI
[2024-01-24 15:28:00,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgf68ee04a-7fcd-44f8-a82c-c7a8de0dc305/GCF_016820635.1_ASM1682063v1_genomic.fna.gz --refList GCF_016820635.1_ASM1682063v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016820635.1_ASM1682063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:08,686] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:08,702] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:08,703] [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_016820635.1	s__Senegalia sp016820635	100.0	884	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016820655.1	s__Senegalia sp016820655	79.6525	443	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911265.1	s__Senegalia massiliensis_A	78.498	331	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626135.1	s__Senegalia massiliensis	78.2646	323	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620125.1	s__Clostridiisalibacter paucivorans	76.8686	114	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Clostridiisalibacteraceae;g__Clostridiisalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711785.1	s__MES13 sp009711785	76.3447	153	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__MES13;g__MES13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000387765.1	s__Caldisalinibacter kiritimatiensis	76.2309	98	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Caldisalinibacteraceae;g__Caldisalinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711765.1	s__MES13 sp009711765	76.1584	164	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__MES13;g__MES13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696605.1	s__Anaerosalibacter bizertensis	76.074	96	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	98.53	98.48	0.86	0.84	3	-
GCF_001316435.1	s__Caloranaerobacter sp001316435	76.0044	95	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000751555.1	s__Anaerosalibacter massiliensis	75.9173	125	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001730685.1	s__Caloranaerobacter ferrireducens	75.8896	99	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107485.1	s__Proteiniborus ethanoligenes	75.758	84	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142235.1	s__Tepidibacter formicigenes	75.6146	102	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Tepidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001584565.1	s__Clostridium_Y paradoxum	75.3272	63	887	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridium_Y	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:08,705] [INFO] GTDB search result was written to GCF_016820635.1_ASM1682063v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:08,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:08,709] [INFO] DFAST_QC result json was written to GCF_016820635.1_ASM1682063v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:08,709] [INFO] DFAST_QC completed!
[2024-01-24 15:28:08,709] [INFO] Total running time: 0h0m47s