[2024-01-24 11:05:34,655] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f24c5b4-844f-4b1f-b8d5-a25393978818/dqc_reference
[2024-01-24 11:05:35,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,871] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,872] [INFO] Running command: gunzip -c /var/lib/cwl/stgc41c12b1-bc47-4ab7-b212-3da3feaeb6d5/GCF_019884785.1_ASM1988478v1_genomic.fna.gz | prodigal -d GCF_019884785.1_ASM1988478v1_genomic.fna/cds.fna -a GCF_019884785.1_ASM1988478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:44,062] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:44,062] [INFO] Task started: HMMsearch
[2024-01-24 11:05:44,063] [INFO] Running command: hmmsearch --tblout GCF_019884785.1_ASM1988478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f24c5b4-844f-4b1f-b8d5-a25393978818/dqc_reference/reference_markers.hmm GCF_019884785.1_ASM1988478v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:44,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:44,411] [INFO] Found 6/6 markers.
[2024-01-24 11:05:44,454] [INFO] Query marker FASTA was written to GCF_019884785.1_ASM1988478v1_genomic.fna/markers.fasta
[2024-01-24 11:05:44,454] [INFO] Task started: Blastn
[2024-01-24 11:05:44,455] [INFO] Running command: blastn -query GCF_019884785.1_ASM1988478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f24c5b4-844f-4b1f-b8d5-a25393978818/dqc_reference/reference_markers.fasta -out GCF_019884785.1_ASM1988478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:45,084] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:45,089] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:45,089] [INFO] Target genome list was writen to GCF_019884785.1_ASM1988478v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:45,110] [INFO] Task started: fastANI
[2024-01-24 11:05:45,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgc41c12b1-bc47-4ab7-b212-3da3feaeb6d5/GCF_019884785.1_ASM1988478v1_genomic.fna.gz --refList GCF_019884785.1_ASM1988478v1_genomic.fna/target_genomes.txt --output GCF_019884785.1_ASM1988478v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:55,453] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:55,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f24c5b4-844f-4b1f-b8d5-a25393978818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:55,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f24c5b4-844f-4b1f-b8d5-a25393978818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:55,468] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:55,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:55,468] [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	100.0	1527	1529	95	conclusive
Crassaminicella thermophila	strain=SY095	GCA_008152325.1	2599308	2599308	type	True	80.3373	555	1529	95	below_threshold
Anaeromicrobium sediminis	strain=DY2726D	GCA_002270055.1	1478221	1478221	type	True	77.3905	241	1529	95	below_threshold
Anaerosolibacter carboniphilus	strain=DSM 103526	GCA_014205875.1	1417629	1417629	type	True	76.3794	128	1529	95	below_threshold
Geosporobacter subterraneus	strain=DSM 17957	GCA_900142145.1	390806	390806	type	True	76.2163	87	1529	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	76.147	103	1529	95	below_threshold
Natronincola peptidivorans	strain=DSM 18979	GCA_900111615.1	426128	426128	type	True	76.0288	62	1529	95	below_threshold
Caminicella sporogenes	strain=AM 1114	GCA_003609595.1	166485	166485	type	True	76.0102	140	1529	95	below_threshold
Caminicella sporogenes	strain=DSM 14501	GCA_900142285.1	166485	166485	type	True	75.8552	137	1529	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	75.8536	147	1529	95	below_threshold
Garciella nitratireducens	strain=DSM 15102	GCA_900167305.1	218205	218205	type	True	75.4452	84	1529	95	below_threshold
Alkaliphilus flagellatus	strain=MSJ-5	GCA_018919215.1	2841507	2841507	type	True	75.3105	90	1529	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.2123	73	1529	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:55,470] [INFO] DFAST Taxonomy check result was written to GCF_019884785.1_ASM1988478v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:55,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:55,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:55,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f24c5b4-844f-4b1f-b8d5-a25393978818/dqc_reference/checkm_data
[2024-01-24 11:05:55,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:55,514] [INFO] Task started: CheckM
[2024-01-24 11:05:55,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019884785.1_ASM1988478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019884785.1_ASM1988478v1_genomic.fna/checkm_input GCF_019884785.1_ASM1988478v1_genomic.fna/checkm_result
[2024-01-24 11:06:26,662] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:26,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:26,690] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:26,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:26,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019884785.1_ASM1988478v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:26,691] [INFO] Task started: Blastn
[2024-01-24 11:06:26,692] [INFO] Running command: blastn -query GCF_019884785.1_ASM1988478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f24c5b4-844f-4b1f-b8d5-a25393978818/dqc_reference/reference_markers_gtdb.fasta -out GCF_019884785.1_ASM1988478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:27,649] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:27,654] [INFO] Selected 16 target genomes.
[2024-01-24 11:06:27,654] [INFO] Target genome list was writen to GCF_019884785.1_ASM1988478v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:27,667] [INFO] Task started: fastANI
[2024-01-24 11:06:27,667] [INFO] Running command: fastANI --query /var/lib/cwl/stgc41c12b1-bc47-4ab7-b212-3da3feaeb6d5/GCF_019884785.1_ASM1988478v1_genomic.fna.gz --refList GCF_019884785.1_ASM1988478v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019884785.1_ASM1988478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:37,634] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:37,646] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:37,646] [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	84.2271	689	1529	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	-
GCF_008152325.1	s__SY095 sp008152325	80.3292	556	1529	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	79.8794	617	1529	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_001282725.1	s__Inediibacterium massiliense	78.6926	433	1529	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_001750685.1	s__Geosporobacter ferrireducens	78.4311	124	1529	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_004138215.1	s__Inediibacterium nitritogenes	78.3695	370	1529	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_002270055.1	s__Anaeromicrobium sediminis	77.3929	240	1529	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_900142235.1	s__Tepidibacter formicigenes	75.852	147	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Tepidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167305.1	s__Garciella nitratireducens	75.4436	84	1529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Garciellaceae;g__Garciella	95.0	99.29	99.29	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:37,647] [INFO] GTDB search result was written to GCF_019884785.1_ASM1988478v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:37,648] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:37,651] [INFO] DFAST_QC result json was written to GCF_019884785.1_ASM1988478v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:37,651] [INFO] DFAST_QC completed!
[2024-01-24 11:06:37,651] [INFO] Total running time: 0h1m3s