[2024-01-24 12:16:07,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:07,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:07,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg93b6c525-6f2f-461b-a133-e9b8d5b193ac/dqc_reference
[2024-01-24 12:16:09,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,336] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg18ba763d-f373-4673-b543-dded5e252dd7/GCF_018919205.1_ASM1891920v1_genomic.fna.gz | prodigal -d GCF_018919205.1_ASM1891920v1_genomic.fna/cds.fna -a GCF_018919205.1_ASM1891920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:19,408] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:19,409] [INFO] Task started: HMMsearch
[2024-01-24 12:16:19,409] [INFO] Running command: hmmsearch --tblout GCF_018919205.1_ASM1891920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93b6c525-6f2f-461b-a133-e9b8d5b193ac/dqc_reference/reference_markers.hmm GCF_018919205.1_ASM1891920v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:19,706] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:19,707] [INFO] Found 6/6 markers.
[2024-01-24 12:16:19,739] [INFO] Query marker FASTA was written to GCF_018919205.1_ASM1891920v1_genomic.fna/markers.fasta
[2024-01-24 12:16:19,740] [INFO] Task started: Blastn
[2024-01-24 12:16:19,740] [INFO] Running command: blastn -query GCF_018919205.1_ASM1891920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b6c525-6f2f-461b-a133-e9b8d5b193ac/dqc_reference/reference_markers.fasta -out GCF_018919205.1_ASM1891920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:20,467] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:20,470] [INFO] Selected 15 target genomes.
[2024-01-24 12:16:20,470] [INFO] Target genome list was writen to GCF_018919205.1_ASM1891920v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:20,477] [INFO] Task started: fastANI
[2024-01-24 12:16:20,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ba763d-f373-4673-b543-dded5e252dd7/GCF_018919205.1_ASM1891920v1_genomic.fna.gz --refList GCF_018919205.1_ASM1891920v1_genomic.fna/target_genomes.txt --output GCF_018919205.1_ASM1891920v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:28,402] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:28,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93b6c525-6f2f-461b-a133-e9b8d5b193ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:28,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93b6c525-6f2f-461b-a133-e9b8d5b193ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:28,416] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:28,417] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:28,417] [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
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	100.0	1050	1053	95	conclusive
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	81.187	148	1053	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	81.0241	144	1053	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	80.8077	142	1053	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.0075	312	1053	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	79.2697	211	1053	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.9116	176	1053	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.8164	212	1053	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.3398	150	1053	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.3242	187	1053	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	78.1855	224	1053	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.9693	175	1053	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.7144	161	1053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:28,418] [INFO] DFAST Taxonomy check result was written to GCF_018919205.1_ASM1891920v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:28,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:28,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:28,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93b6c525-6f2f-461b-a133-e9b8d5b193ac/dqc_reference/checkm_data
[2024-01-24 12:16:28,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:28,459] [INFO] Task started: CheckM
[2024-01-24 12:16:28,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018919205.1_ASM1891920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018919205.1_ASM1891920v1_genomic.fna/checkm_input GCF_018919205.1_ASM1891920v1_genomic.fna/checkm_result
[2024-01-24 12:17:01,695] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:01,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:01,718] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:01,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:01,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018919205.1_ASM1891920v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:01,719] [INFO] Task started: Blastn
[2024-01-24 12:17:01,720] [INFO] Running command: blastn -query GCF_018919205.1_ASM1891920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b6c525-6f2f-461b-a133-e9b8d5b193ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_018919205.1_ASM1891920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:03,013] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:03,018] [INFO] Selected 20 target genomes.
[2024-01-24 12:17:03,019] [INFO] Target genome list was writen to GCF_018919205.1_ASM1891920v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:03,034] [INFO] Task started: fastANI
[2024-01-24 12:17:03,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ba763d-f373-4673-b543-dded5e252dd7/GCF_018919205.1_ASM1891920v1_genomic.fna.gz --refList GCF_018919205.1_ASM1891920v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018919205.1_ASM1891920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:13,190] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:13,205] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:13,206] [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_018919205.1	s__NSJ-62 sp018919205	100.0	1050	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-62	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014334055.1	s__NSJ-62 sp014334055	91.3218	728	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-62	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	80.065	305	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCF_018228705.1	s__Dysosmobacter sp018228705	79.8556	347	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118505.1	s__Dysosmobacter excrementavium	79.5989	288	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544955.1	s__Dysosmobacter sp900544955	79.5896	294	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	79.5823	306	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	79.3371	297	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018408705.1	s__Dysosmobacter sp014297375	79.2933	210	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.15	98.99	0.84	0.71	5	-
GCA_017469475.1	s__Dysosmobacter sp017469475	79.2819	245	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.68	97.62	0.84	0.82	4	-
GCA_900546705.1	s__Dysosmobacter sp900546705	79.0833	252	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436875.1	s__Dysosmobacter sp000436875	79.0338	251	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.76	95.67	0.88	0.85	3	-
GCA_900548505.1	s__Dysosmobacter sp900548505	79.0191	260	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579435.1	s__Dysosmobacter sp910579435	78.6809	243	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579365.1	s__Dysosmobacter sp910579365	78.4372	247	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161215.1	s__Flavonifractor avistercoris	78.2753	226	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_000283575.1	s__Oscillibacter valericigenes	78.178	221	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004560375.1	s__Enterenecus sp004560375	78.0423	143	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117605.1	s__Intestinimonas stercoravium	77.6879	154	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.97	98.96	0.85	0.84	3	-
GCA_019119165.1	s__Flavonifractor intestinigallinarum	77.5194	145	1053	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.85	97.85	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:13,208] [INFO] GTDB search result was written to GCF_018919205.1_ASM1891920v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:13,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:13,213] [INFO] DFAST_QC result json was written to GCF_018919205.1_ASM1891920v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:13,213] [INFO] DFAST_QC completed!
[2024-01-24 12:17:13,213] [INFO] Total running time: 0h1m5s