[2024-01-24 13:36:32,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,153] [INFO] DQC Reference Directory: /var/lib/cwl/stge33a6ce2-476d-4593-aa5f-44eae652e444/dqc_reference
[2024-01-24 13:36:33,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,458] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg868ca250-7cf7-4932-a33d-f072aa85222c/GCF_014297285.1_ASM1429728v1_genomic.fna.gz | prodigal -d GCF_014297285.1_ASM1429728v1_genomic.fna/cds.fna -a GCF_014297285.1_ASM1429728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:43,790] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:43,791] [INFO] Task started: HMMsearch
[2024-01-24 13:36:43,791] [INFO] Running command: hmmsearch --tblout GCF_014297285.1_ASM1429728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge33a6ce2-476d-4593-aa5f-44eae652e444/dqc_reference/reference_markers.hmm GCF_014297285.1_ASM1429728v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:44,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:44,096] [INFO] Found 6/6 markers.
[2024-01-24 13:36:44,133] [INFO] Query marker FASTA was written to GCF_014297285.1_ASM1429728v1_genomic.fna/markers.fasta
[2024-01-24 13:36:44,134] [INFO] Task started: Blastn
[2024-01-24 13:36:44,134] [INFO] Running command: blastn -query GCF_014297285.1_ASM1429728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge33a6ce2-476d-4593-aa5f-44eae652e444/dqc_reference/reference_markers.fasta -out GCF_014297285.1_ASM1429728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:44,820] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:44,823] [INFO] Selected 12 target genomes.
[2024-01-24 13:36:44,823] [INFO] Target genome list was writen to GCF_014297285.1_ASM1429728v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:44,830] [INFO] Task started: fastANI
[2024-01-24 13:36:44,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg868ca250-7cf7-4932-a33d-f072aa85222c/GCF_014297285.1_ASM1429728v1_genomic.fna.gz --refList GCF_014297285.1_ASM1429728v1_genomic.fna/target_genomes.txt --output GCF_014297285.1_ASM1429728v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:51,114] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:51,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge33a6ce2-476d-4593-aa5f-44eae652e444/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:51,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge33a6ce2-476d-4593-aa5f-44eae652e444/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:51,127] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:36:51,127] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:36:51,127] [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
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	82.0875	121	1168	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	81.9483	124	1168	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.9468	407	1168	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	80.6355	249	1168	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	80.0832	203	1168	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	80.0674	257	1168	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	79.2733	256	1168	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.667	147	1168	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.6212	149	1168	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	78.5255	207	1168	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.3513	147	1168	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.2636	141	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:51,129] [INFO] DFAST Taxonomy check result was written to GCF_014297285.1_ASM1429728v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:51,130] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:51,130] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:51,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge33a6ce2-476d-4593-aa5f-44eae652e444/dqc_reference/checkm_data
[2024-01-24 13:36:51,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:51,178] [INFO] Task started: CheckM
[2024-01-24 13:36:51,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014297285.1_ASM1429728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014297285.1_ASM1429728v1_genomic.fna/checkm_input GCF_014297285.1_ASM1429728v1_genomic.fna/checkm_result
[2024-01-24 13:37:26,948] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:26,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:26,990] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:26,990] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:26,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014297285.1_ASM1429728v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:26,991] [INFO] Task started: Blastn
[2024-01-24 13:37:26,991] [INFO] Running command: blastn -query GCF_014297285.1_ASM1429728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge33a6ce2-476d-4593-aa5f-44eae652e444/dqc_reference/reference_markers_gtdb.fasta -out GCF_014297285.1_ASM1429728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:28,345] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:28,349] [INFO] Selected 8 target genomes.
[2024-01-24 13:37:28,349] [INFO] Target genome list was writen to GCF_014297285.1_ASM1429728v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:28,358] [INFO] Task started: fastANI
[2024-01-24 13:37:28,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg868ca250-7cf7-4932-a33d-f072aa85222c/GCF_014297285.1_ASM1429728v1_genomic.fna.gz --refList GCF_014297285.1_ASM1429728v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014297285.1_ASM1429728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:33,785] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:33,793] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:33,793] [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_014297285.1	s__Dysosmobacter sp001916835	100.0	1162	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	96.98	96.30	0.86	0.70	9	conclusive
GCA_900544105.1	s__Dysosmobacter sp900544105	94.014	530	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.36	97.36	0.83	0.83	2	-
GCA_900550685.1	s__Dysosmobacter sp900550685	85.9862	383	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.83	98.83	0.76	0.76	2	-
GCA_900544615.1	s__Dysosmobacter sp900544615	85.4844	480	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900542115.1	s__Dysosmobacter sp900542115	85.2036	386	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.37	98.19	0.79	0.78	3	-
GCA_004558115.1	s__Dysosmobacter sp004558115	80.9745	275	1168	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	80.7106	353	1168	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_017937405.1	s__Dysosmobacter sp017937405	80.3542	331	1168	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:33,795] [INFO] GTDB search result was written to GCF_014297285.1_ASM1429728v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:33,796] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:33,800] [INFO] DFAST_QC result json was written to GCF_014297285.1_ASM1429728v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:33,800] [INFO] DFAST_QC completed!
[2024-01-24 13:37:33,800] [INFO] Total running time: 0h1m2s