[2024-01-25 19:49:20,608] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:20,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:20,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg25ec41bf-93cc-42ca-b61f-546d3fdba4ae/dqc_reference
[2024-01-25 19:49:21,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:21,818] [INFO] Task started: Prodigal
[2024-01-25 19:49:21,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3f00a19-2731-4a89-a298-efcbed50ee33/GCF_030812875.1_ASM3081287v1_genomic.fna.gz | prodigal -d GCF_030812875.1_ASM3081287v1_genomic.fna/cds.fna -a GCF_030812875.1_ASM3081287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:24,605] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:24,605] [INFO] Task started: HMMsearch
[2024-01-25 19:49:24,606] [INFO] Running command: hmmsearch --tblout GCF_030812875.1_ASM3081287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25ec41bf-93cc-42ca-b61f-546d3fdba4ae/dqc_reference/reference_markers.hmm GCF_030812875.1_ASM3081287v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:24,780] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:24,782] [INFO] Found 6/6 markers.
[2024-01-25 19:49:24,800] [INFO] Query marker FASTA was written to GCF_030812875.1_ASM3081287v1_genomic.fna/markers.fasta
[2024-01-25 19:49:24,800] [INFO] Task started: Blastn
[2024-01-25 19:49:24,800] [INFO] Running command: blastn -query GCF_030812875.1_ASM3081287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25ec41bf-93cc-42ca-b61f-546d3fdba4ae/dqc_reference/reference_markers.fasta -out GCF_030812875.1_ASM3081287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:25,332] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:25,337] [INFO] Selected 18 target genomes.
[2024-01-25 19:49:25,337] [INFO] Target genome list was writen to GCF_030812875.1_ASM3081287v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:25,357] [INFO] Task started: fastANI
[2024-01-25 19:49:25,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3f00a19-2731-4a89-a298-efcbed50ee33/GCF_030812875.1_ASM3081287v1_genomic.fna.gz --refList GCF_030812875.1_ASM3081287v1_genomic.fna/target_genomes.txt --output GCF_030812875.1_ASM3081287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:30,534] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:30,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25ec41bf-93cc-42ca-b61f-546d3fdba4ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:30,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25ec41bf-93cc-42ca-b61f-546d3fdba4ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:30,544] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:49:30,544] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:49:30,544] [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
Peptoniphilus grossensis	strain=ph5	GCA_000311825.1	1465756	1465756	type	True	82.9329	121	590	95	below_threshold
Peptoniphilus lacrimalis	strain=NCTC13149	GCA_900454715.1	33031	33031	type	True	81.7643	122	590	95	below_threshold
Peptoniphilus lacrimalis	strain=DSM 7455	GCA_000378725.1	33031	33031	type	True	81.7256	123	590	95	below_threshold
Peptoniphilus harei	strain=FDAARGOS_1136	GCA_016726485.1	54005	54005	suspected-type	True	81.1567	80	590	95	below_threshold
Peptoniphilus gorbachii	strain=DSM 21461	GCA_016908115.1	411567	411567	type	True	80.969	125	590	95	below_threshold
Peptoniphilus obesi	strain=ph1	GCA_000311865.1	1472765	1472765	type	True	80.8787	109	590	95	below_threshold
Peptoniphilus harei	strain=NCTC13076	GCA_900454685.1	54005	54005	suspected-type	True	80.8138	86	590	95	below_threshold
Peptoniphilus asaccharolyticus	strain=FDAARGOS_1135	GCA_016791605.1	1258	1258	type	True	80.6168	84	590	95	below_threshold
Peptoniphilus phoceensis	strain=SIT15	GCA_001517665.2	1720298	1720298	type	True	80.0588	92	590	95	below_threshold
Anaerosphaera multitolerans	strain=GS7-6-2	GCA_004006535.1	2487351	2487351	type	True	78.8684	70	590	95	below_threshold
Anaerosphaera aminiphila	strain=DSM 21120	GCA_900129925.1	1120994	1120994	type	True	78.6902	66	590	95	below_threshold
Peptoniphilus timonensis	strain=JC401	GCA_000312025.1	1268254	1268254	type	True	78.3796	95	590	95	below_threshold
Peptoniphilus stercorisuis	strain=DSM 27563	GCA_017874395.1	1436965	1436965	type	True	76.6734	79	590	95	below_threshold
Peptoniphilus mikwangii	strain=ChDC B134	GCA_000468535.1	1354300	1354300	type	True	76.5679	79	590	95	below_threshold
Anaerosphaera massiliensis	strain=Marseille-P4592	GCA_902167235.1	2040296	2040296	type	True	75.8794	69	590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:30,546] [INFO] DFAST Taxonomy check result was written to GCF_030812875.1_ASM3081287v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:30,546] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:30,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:30,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25ec41bf-93cc-42ca-b61f-546d3fdba4ae/dqc_reference/checkm_data
[2024-01-25 19:49:30,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:30,569] [INFO] Task started: CheckM
[2024-01-25 19:49:30,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030812875.1_ASM3081287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030812875.1_ASM3081287v1_genomic.fna/checkm_input GCF_030812875.1_ASM3081287v1_genomic.fna/checkm_result
[2024-01-25 19:49:45,608] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:45,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:45,624] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:45,624] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:45,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030812875.1_ASM3081287v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:45,624] [INFO] Task started: Blastn
[2024-01-25 19:49:45,625] [INFO] Running command: blastn -query GCF_030812875.1_ASM3081287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25ec41bf-93cc-42ca-b61f-546d3fdba4ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_030812875.1_ASM3081287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:46,358] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:46,361] [INFO] Selected 20 target genomes.
[2024-01-25 19:49:46,361] [INFO] Target genome list was writen to GCF_030812875.1_ASM3081287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:46,374] [INFO] Task started: fastANI
[2024-01-25 19:49:46,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3f00a19-2731-4a89-a298-efcbed50ee33/GCF_030812875.1_ASM3081287v1_genomic.fna.gz --refList GCF_030812875.1_ASM3081287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030812875.1_ASM3081287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:55,036] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:55,046] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:55,046] [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_000478985.1	s__Peptoniphilus_B sp000478985	99.3753	560	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000146345.1	s__Peptoniphilus_B duerdenii	83.725	145	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_B	95.0	96.19	96.19	0.86	0.86	2	-
GCF_000378725.1	s__Peptoniphilus_A lacrimalis	81.7256	123	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	98.41	97.10	0.92	0.86	4	-
GCF_016908115.1	s__Peptoniphilus_A gorbachii	80.9176	126	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	96.70	96.17	0.85	0.82	5	-
GCF_000311865.1	s__Peptoniphilus_E obesi	80.8787	109	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900454685.1	s__Peptoniphilus_A harei	80.8748	85	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.43	96.58	0.91	0.87	7	-
GCF_900176115.1	s__Peptoniphilus asaccharolyticus	80.6429	84	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_001517665.2	s__Peptoniphilus_A phoceensis	80.0232	91	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	100.00	100.00	1.00	1.00	2	-
GCF_004006535.1	s__Anaerosphaera multitolerans	78.8684	70	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129925.1	s__Anaerosphaera aminiphila	78.6902	66	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312025.1	s__Peptoniphilus_A timonensis	78.3796	95	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	N/A	N/A	N/A	N/A	1	-
GCF_017874395.1	s__Anaerosphaera stercorisuis	76.6451	80	590	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:55,047] [INFO] GTDB search result was written to GCF_030812875.1_ASM3081287v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:55,048] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:55,051] [INFO] DFAST_QC result json was written to GCF_030812875.1_ASM3081287v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:55,051] [INFO] DFAST_QC completed!
[2024-01-25 19:49:55,051] [INFO] Total running time: 0h0m34s