[2024-01-24 13:47:10,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:10,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:10,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg405aac7b-85cb-4cb3-8b2c-5a62992b309b/dqc_reference
[2024-01-24 13:47:11,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:11,917] [INFO] Task started: Prodigal
[2024-01-24 13:47:11,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bf7dd71-7048-49d8-8864-00ff054f667f/GCF_000321165.1_ASM32116v1_genomic.fna.gz | prodigal -d GCF_000321165.1_ASM32116v1_genomic.fna/cds.fna -a GCF_000321165.1_ASM32116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:18,936] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:18,936] [INFO] Task started: HMMsearch
[2024-01-24 13:47:18,936] [INFO] Running command: hmmsearch --tblout GCF_000321165.1_ASM32116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg405aac7b-85cb-4cb3-8b2c-5a62992b309b/dqc_reference/reference_markers.hmm GCF_000321165.1_ASM32116v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:19,166] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:19,167] [INFO] Found 6/6 markers.
[2024-01-24 13:47:19,203] [INFO] Query marker FASTA was written to GCF_000321165.1_ASM32116v1_genomic.fna/markers.fasta
[2024-01-24 13:47:19,204] [INFO] Task started: Blastn
[2024-01-24 13:47:19,204] [INFO] Running command: blastn -query GCF_000321165.1_ASM32116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg405aac7b-85cb-4cb3-8b2c-5a62992b309b/dqc_reference/reference_markers.fasta -out GCF_000321165.1_ASM32116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:20,017] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:20,022] [INFO] Selected 12 target genomes.
[2024-01-24 13:47:20,022] [INFO] Target genome list was writen to GCF_000321165.1_ASM32116v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:20,042] [INFO] Task started: fastANI
[2024-01-24 13:47:20,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf7dd71-7048-49d8-8864-00ff054f667f/GCF_000321165.1_ASM32116v1_genomic.fna.gz --refList GCF_000321165.1_ASM32116v1_genomic.fna/target_genomes.txt --output GCF_000321165.1_ASM32116v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:25,813] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:25,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg405aac7b-85cb-4cb3-8b2c-5a62992b309b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:25,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg405aac7b-85cb-4cb3-8b2c-5a62992b309b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:25,823] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:25,823] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:25,824] [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
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	100.0	713	718	95	conclusive
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	83.9749	426	718	95	below_threshold
Enorma massiliensis		GCA_000311845.1	1472761	1472761	type	True	82.1065	382	718	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	81.8803	391	718	95	below_threshold
Enorma phocaeensis	strain=Marseille-P3242	GCA_900186505.1	1871019	1871019	type	True	81.8103	366	718	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.502	293	718	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.4723	292	718	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.4422	294	718	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.6596	243	718	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.5785	262	718	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.477	259	718	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	78.3506	193	718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:25,838] [INFO] DFAST Taxonomy check result was written to GCF_000321165.1_ASM32116v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:25,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:25,839] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:25,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg405aac7b-85cb-4cb3-8b2c-5a62992b309b/dqc_reference/checkm_data
[2024-01-24 13:47:25,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:25,871] [INFO] Task started: CheckM
[2024-01-24 13:47:25,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000321165.1_ASM32116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000321165.1_ASM32116v1_genomic.fna/checkm_input GCF_000321165.1_ASM32116v1_genomic.fna/checkm_result
[2024-01-24 13:47:50,464] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:50,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:50,484] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:50,484] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:50,485] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000321165.1_ASM32116v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:50,485] [INFO] Task started: Blastn
[2024-01-24 13:47:50,485] [INFO] Running command: blastn -query GCF_000321165.1_ASM32116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg405aac7b-85cb-4cb3-8b2c-5a62992b309b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000321165.1_ASM32116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:51,757] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:51,761] [INFO] Selected 11 target genomes.
[2024-01-24 13:47:51,762] [INFO] Target genome list was writen to GCF_000321165.1_ASM32116v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:51,775] [INFO] Task started: fastANI
[2024-01-24 13:47:51,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf7dd71-7048-49d8-8864-00ff054f667f/GCF_000321165.1_ASM32116v1_genomic.fna.gz --refList GCF_000321165.1_ASM32116v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000321165.1_ASM32116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:56,981] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:56,996] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:56,997] [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_000333815.1	s__Enorma sp000333815	99.9589	682	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	conclusive
GCA_900538305.1	s__Enorma sp900538305	84.2353	456	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210055.1	s__Enorma sp900751795	84.2013	391	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	99.77	99.77	0.84	0.84	2	-
GCF_902150035.1	s__Enorma burkinafasonensis	84.0145	424	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000311845.1	s__Enorma massiliensis	82.0926	383	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	97.43	96.04	0.89	0.84	11	-
GCF_900186505.1	s__Enorma phocaeensis	81.8025	367	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117005.1	s__Collinsella stercoripullorum	81.7154	355	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCF_002159765.1	s__Coprousia sp002159765	81.4382	352	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	97.90	97.74	0.89	0.88	3	-
GCA_018715125.1	s__Coprousia avicola	81.1908	336	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160065.1	s__Limicola sp002160065	80.8642	325	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014645.1	s__Collinsella sp008014645	80.1152	244	718	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:56,998] [INFO] GTDB search result was written to GCF_000321165.1_ASM32116v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:56,999] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:57,002] [INFO] DFAST_QC result json was written to GCF_000321165.1_ASM32116v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:57,002] [INFO] DFAST_QC completed!
[2024-01-24 13:47:57,002] [INFO] Total running time: 0h0m46s