[2024-01-24 12:22:48,485] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg22bb7965-7e6b-424c-8c2a-73ce469561bb/dqc_reference
[2024-01-24 12:22:49,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,916] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,916] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1881fa3-7329-4473-bac1-31421faff983/GCF_016820655.1_ASM1682065v1_genomic.fna.gz | prodigal -d GCF_016820655.1_ASM1682065v1_genomic.fna/cds.fna -a GCF_016820655.1_ASM1682065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:54,884] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:54,884] [INFO] Task started: HMMsearch
[2024-01-24 12:22:54,885] [INFO] Running command: hmmsearch --tblout GCF_016820655.1_ASM1682065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22bb7965-7e6b-424c-8c2a-73ce469561bb/dqc_reference/reference_markers.hmm GCF_016820655.1_ASM1682065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:55,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:55,167] [INFO] Found 6/6 markers.
[2024-01-24 12:22:55,209] [INFO] Query marker FASTA was written to GCF_016820655.1_ASM1682065v1_genomic.fna/markers.fasta
[2024-01-24 12:22:55,210] [INFO] Task started: Blastn
[2024-01-24 12:22:55,210] [INFO] Running command: blastn -query GCF_016820655.1_ASM1682065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22bb7965-7e6b-424c-8c2a-73ce469561bb/dqc_reference/reference_markers.fasta -out GCF_016820655.1_ASM1682065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:55,822] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:55,825] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:55,825] [INFO] Target genome list was writen to GCF_016820655.1_ASM1682065v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:55,832] [INFO] Task started: fastANI
[2024-01-24 12:22:55,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1881fa3-7329-4473-bac1-31421faff983/GCF_016820655.1_ASM1682065v1_genomic.fna.gz --refList GCF_016820655.1_ASM1682065v1_genomic.fna/target_genomes.txt --output GCF_016820655.1_ASM1682065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:03,681] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:03,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22bb7965-7e6b-424c-8c2a-73ce469561bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:03,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22bb7965-7e6b-424c-8c2a-73ce469561bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:03,693] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:03,693] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:03,693] [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 frigoriresistens	strain=D2Q-11	GCA_016820655.1	2683708	2683708	type	True	100.0	1044	1048	95	conclusive
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	79.8361	435	1048	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	78.324	328	1048	95	below_threshold
Caloranaerobacter azorensis	strain=DSM 13643	GCA_900129995.1	116090	116090	type	True	76.5659	87	1048	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	76.2919	126	1048	95	below_threshold
Clostridiisalibacter paucivorans	strain=DSM 22131	GCA_000620125.1	408753	408753	type	True	76.1193	118	1048	95	below_threshold
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	75.6207	68	1048	95	below_threshold
Gottschalkia acidurici	strain=9a	GCA_000299355.1	1556	1556	type	True	75.6081	80	1048	95	below_threshold
Sporanaerobacter acetigenes	strain=DSM 13106	GCA_900130025.1	165813	165813	type	True	75.5809	86	1048	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	75.5374	60	1048	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	75.5178	108	1048	95	below_threshold
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	75.516	59	1048	95	below_threshold
Gottschalkia purinilytica	strain=DSM 1384	GCA_001190785.1	1503	1503	type	True	75.5009	100	1048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:03,695] [INFO] DFAST Taxonomy check result was written to GCF_016820655.1_ASM1682065v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:03,695] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:03,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:03,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22bb7965-7e6b-424c-8c2a-73ce469561bb/dqc_reference/checkm_data
[2024-01-24 12:23:03,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:03,730] [INFO] Task started: CheckM
[2024-01-24 12:23:03,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016820655.1_ASM1682065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016820655.1_ASM1682065v1_genomic.fna/checkm_input GCF_016820655.1_ASM1682065v1_genomic.fna/checkm_result
[2024-01-24 12:23:26,094] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:26,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:26,120] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:26,121] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:26,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016820655.1_ASM1682065v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:26,122] [INFO] Task started: Blastn
[2024-01-24 12:23:26,122] [INFO] Running command: blastn -query GCF_016820655.1_ASM1682065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22bb7965-7e6b-424c-8c2a-73ce469561bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016820655.1_ASM1682065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:26,876] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:26,880] [INFO] Selected 18 target genomes.
[2024-01-24 12:23:26,880] [INFO] Target genome list was writen to GCF_016820655.1_ASM1682065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:26,911] [INFO] Task started: fastANI
[2024-01-24 12:23:26,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1881fa3-7329-4473-bac1-31421faff983/GCF_016820655.1_ASM1682065v1_genomic.fna.gz --refList GCF_016820655.1_ASM1682065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016820655.1_ASM1682065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:35,488] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:35,505] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:35,506] [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_016820655.1	s__Senegalia sp016820655	100.0	1044	1048	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_016820635.1	s__Senegalia sp016820635	79.8361	435	1048	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	78.3131	329	1048	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	78.0683	341	1048	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_900129995.1	s__Caloranaerobacter azorensis	76.5659	87	1048	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	97.96	97.93	0.87	0.85	4	-
GCF_016765695.1	s__Sporosalibacterium faouarense	76.2919	126	1048	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__VENL01;g__Sporosalibacterium	95.0	99.35	99.35	0.89	0.89	2	-
GCF_000620125.1	s__Clostridiisalibacter paucivorans	76.1193	118	1048	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_009711765.1	s__MES13 sp009711765	76.0297	159	1048	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__MES13;g__MES13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711785.1	s__MES13 sp009711785	76.0061	164	1048	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_000299355.1	s__Gottschalkia acidurici	75.6081	80	1048	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Gottschalkiaceae;g__Gottschalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130025.1	s__Sporanaerobacter acetigenes	75.5809	86	1048	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Sporanaerobacter	95.0	99.49	99.49	0.90	0.90	2	-
GCF_016767175.1	s__Keratinibaculum paraultunense	75.516	59	1048	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001190785.1	s__Gottschalkia_A purinilytica	75.5009	100	1048	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Gottschalkiaceae;g__Gottschalkia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904418825.1	s__Romboutsia sp904418825	75.2739	65	1048	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	99.17	99.17	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:35,507] [INFO] GTDB search result was written to GCF_016820655.1_ASM1682065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:35,508] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:35,512] [INFO] DFAST_QC result json was written to GCF_016820655.1_ASM1682065v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:35,513] [INFO] DFAST_QC completed!
[2024-01-24 12:23:35,513] [INFO] Total running time: 0h0m47s