[2024-01-24 12:47:49,700] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:49,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:49,701] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0e5e9a3-1a85-418e-b516-3c3d54954c8e/dqc_reference
[2024-01-24 12:47:50,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,901] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,901] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfc9f36c-b123-4f0c-b2c4-b873ff08230e/GCF_019203185.1_ASM1920318v1_genomic.fna.gz | prodigal -d GCF_019203185.1_ASM1920318v1_genomic.fna/cds.fna -a GCF_019203185.1_ASM1920318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:55,632] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:55,633] [INFO] Task started: HMMsearch
[2024-01-24 12:47:55,633] [INFO] Running command: hmmsearch --tblout GCF_019203185.1_ASM1920318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0e5e9a3-1a85-418e-b516-3c3d54954c8e/dqc_reference/reference_markers.hmm GCF_019203185.1_ASM1920318v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:55,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:55,878] [INFO] Found 6/6 markers.
[2024-01-24 12:47:55,903] [INFO] Query marker FASTA was written to GCF_019203185.1_ASM1920318v1_genomic.fna/markers.fasta
[2024-01-24 12:47:55,904] [INFO] Task started: Blastn
[2024-01-24 12:47:55,904] [INFO] Running command: blastn -query GCF_019203185.1_ASM1920318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0e5e9a3-1a85-418e-b516-3c3d54954c8e/dqc_reference/reference_markers.fasta -out GCF_019203185.1_ASM1920318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:56,488] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:56,492] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:56,492] [INFO] Target genome list was writen to GCF_019203185.1_ASM1920318v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:56,535] [INFO] Task started: fastANI
[2024-01-24 12:47:56,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfc9f36c-b123-4f0c-b2c4-b873ff08230e/GCF_019203185.1_ASM1920318v1_genomic.fna.gz --refList GCF_019203185.1_ASM1920318v1_genomic.fna/target_genomes.txt --output GCF_019203185.1_ASM1920318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:08,680] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:08,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0e5e9a3-1a85-418e-b516-3c3d54954c8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:08,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0e5e9a3-1a85-418e-b516-3c3d54954c8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:08,696] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:48:08,697] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:48:08,697] [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
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	84.2449	682	918	95	below_threshold
Crassaminicella thermophila	strain=SY095	GCA_008152325.1	2599308	2599308	type	True	81.1063	497	918	95	below_threshold
Geosporobacter ferrireducens	strain=IRF9	GCA_001750685.1	1424294	1424294	type	True	78.9623	84	918	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	77.9979	90	918	95	below_threshold
Anaeromicrobium sediminis	strain=DY2726D	GCA_002270055.1	1478221	1478221	type	True	77.097	149	918	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	77.0858	65	918	95	below_threshold
Geosporobacter subterraneus	strain=DSM 17957	GCA_900142145.1	390806	390806	type	True	76.8599	85	918	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	76.3979	93	918	95	below_threshold
Garciella nitratireducens	strain=DSM 15102	GCA_900167305.1	218205	218205	type	True	76.0355	73	918	95	below_threshold
Maledivibacter halophilus	strain=M1	GCA_900167445.1	36842	36842	type	True	75.9751	112	918	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	75.8763	73	918	95	below_threshold
Clostridiisalibacter paucivorans	strain=DSM 22131	GCA_000620125.1	408753	408753	type	True	75.8057	62	918	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	75.7706	60	918	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.5782	74	918	95	below_threshold
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	75.5776	56	918	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	75.3	77	918	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:08,699] [INFO] DFAST Taxonomy check result was written to GCF_019203185.1_ASM1920318v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:08,700] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:08,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:08,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0e5e9a3-1a85-418e-b516-3c3d54954c8e/dqc_reference/checkm_data
[2024-01-24 12:48:08,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:08,734] [INFO] Task started: CheckM
[2024-01-24 12:48:08,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019203185.1_ASM1920318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019203185.1_ASM1920318v1_genomic.fna/checkm_input GCF_019203185.1_ASM1920318v1_genomic.fna/checkm_result
[2024-01-24 12:48:30,116] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:30,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:30,145] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:30,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:30,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019203185.1_ASM1920318v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:30,146] [INFO] Task started: Blastn
[2024-01-24 12:48:30,146] [INFO] Running command: blastn -query GCF_019203185.1_ASM1920318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0e5e9a3-1a85-418e-b516-3c3d54954c8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019203185.1_ASM1920318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:30,960] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:30,964] [INFO] Selected 13 target genomes.
[2024-01-24 12:48:30,964] [INFO] Target genome list was writen to GCF_019203185.1_ASM1920318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:30,984] [INFO] Task started: fastANI
[2024-01-24 12:48:30,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfc9f36c-b123-4f0c-b2c4-b873ff08230e/GCF_019203185.1_ASM1920318v1_genomic.fna.gz --refList GCF_019203185.1_ASM1920318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019203185.1_ASM1920318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:39,916] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:39,932] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:39,932] [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_019203185.1	s__143-21 sp019203185	100.0	918	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__143-21	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008152325.1	s__SY095 sp008152325	81.1017	500	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__SY095	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345705.1	s__Marinisporobacter balticus	79.3086	452	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Marinisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750685.1	s__Geosporobacter ferrireducens	79.0941	85	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Geosporobacter	95.0	99.59	99.59	0.96	0.96	2	-
GCF_001282725.1	s__Inediibacterium massiliense	78.7315	360	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Inediibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138215.1	s__Inediibacterium nitritogenes	78.1367	314	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Inediibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686845.1	s__JADPRS01 sp015686845	77.4933	239	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__JADPRS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002270055.1	s__Anaeromicrobium sediminis	77.0796	150	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Anaeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626135.1	s__Senegalia massiliensis	76.3799	93	918	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_900167445.1	s__Maledivibacter halophilus	75.9565	110	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Maledivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620125.1	s__Clostridiisalibacter paucivorans	75.8057	62	918	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_910588715.1	s__Clostridium sp910588715	75.052	60	918	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:39,934] [INFO] GTDB search result was written to GCF_019203185.1_ASM1920318v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:39,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:39,938] [INFO] DFAST_QC result json was written to GCF_019203185.1_ASM1920318v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:39,938] [INFO] DFAST_QC completed!
[2024-01-24 12:48:39,938] [INFO] Total running time: 0h0m50s