[2023-06-13 22:41:34,842] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:41:34,844] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:41:34,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg530c7f55-398c-467d-b349-3867ddec3eeb/dqc_reference
[2023-06-13 22:41:36,033] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:41:36,034] [INFO] Task started: Prodigal
[2023-06-13 22:41:36,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg27263d77-a783-4e90-a334-92919fc21c50/GCA_022767075.1_ASM2276707v1_genomic.fna.gz | prodigal -d GCA_022767075.1_ASM2276707v1_genomic.fna/cds.fna -a GCA_022767075.1_ASM2276707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:41:40,825] [INFO] Task succeeded: Prodigal
[2023-06-13 22:41:40,826] [INFO] Task started: HMMsearch
[2023-06-13 22:41:40,826] [INFO] Running command: hmmsearch --tblout GCA_022767075.1_ASM2276707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg530c7f55-398c-467d-b349-3867ddec3eeb/dqc_reference/reference_markers.hmm GCA_022767075.1_ASM2276707v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:41:41,005] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:41:41,007] [INFO] Found 6/6 markers.
[2023-06-13 22:41:41,036] [INFO] Query marker FASTA was written to GCA_022767075.1_ASM2276707v1_genomic.fna/markers.fasta
[2023-06-13 22:41:41,036] [INFO] Task started: Blastn
[2023-06-13 22:41:41,037] [INFO] Running command: blastn -query GCA_022767075.1_ASM2276707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg530c7f55-398c-467d-b349-3867ddec3eeb/dqc_reference/reference_markers.fasta -out GCA_022767075.1_ASM2276707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:41:41,621] [INFO] Task succeeded: Blastn
[2023-06-13 22:41:41,629] [INFO] Selected 27 target genomes.
[2023-06-13 22:41:41,629] [INFO] Target genome list was writen to GCA_022767075.1_ASM2276707v1_genomic.fna/target_genomes.txt
[2023-06-13 22:41:41,631] [INFO] Task started: fastANI
[2023-06-13 22:41:41,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg27263d77-a783-4e90-a334-92919fc21c50/GCA_022767075.1_ASM2276707v1_genomic.fna.gz --refList GCA_022767075.1_ASM2276707v1_genomic.fna/target_genomes.txt --output GCA_022767075.1_ASM2276707v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:41:57,665] [INFO] Task succeeded: fastANI
[2023-06-13 22:41:57,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg530c7f55-398c-467d-b349-3867ddec3eeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:41:57,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg530c7f55-398c-467d-b349-3867ddec3eeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:41:57,672] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:41:57,673] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:41:57,673] [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
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.479	98	614	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.977	76	614	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.6106	73	614	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.4497	78	614	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.4469	78	614	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.4354	77	614	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:41:57,675] [INFO] DFAST Taxonomy check result was written to GCA_022767075.1_ASM2276707v1_genomic.fna/tc_result.tsv
[2023-06-13 22:41:57,676] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:41:57,676] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:41:57,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg530c7f55-398c-467d-b349-3867ddec3eeb/dqc_reference/checkm_data
[2023-06-13 22:41:57,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:41:57,700] [INFO] Task started: CheckM
[2023-06-13 22:41:57,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022767075.1_ASM2276707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022767075.1_ASM2276707v1_genomic.fna/checkm_input GCA_022767075.1_ASM2276707v1_genomic.fna/checkm_result
[2023-06-13 22:42:18,514] [INFO] Task succeeded: CheckM
[2023-06-13 22:42:18,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 22:42:18,540] [INFO] ===== Completeness check finished =====
[2023-06-13 22:42:18,540] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:42:18,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022767075.1_ASM2276707v1_genomic.fna/markers.fasta)
[2023-06-13 22:42:18,541] [INFO] Task started: Blastn
[2023-06-13 22:42:18,541] [INFO] Running command: blastn -query GCA_022767075.1_ASM2276707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg530c7f55-398c-467d-b349-3867ddec3eeb/dqc_reference/reference_markers_gtdb.fasta -out GCA_022767075.1_ASM2276707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:42:19,359] [INFO] Task succeeded: Blastn
[2023-06-13 22:42:19,364] [INFO] Selected 27 target genomes.
[2023-06-13 22:42:19,364] [INFO] Target genome list was writen to GCA_022767075.1_ASM2276707v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:42:19,368] [INFO] Task started: fastANI
[2023-06-13 22:42:19,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg27263d77-a783-4e90-a334-92919fc21c50/GCA_022767075.1_ASM2276707v1_genomic.fna.gz --refList GCA_022767075.1_ASM2276707v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022767075.1_ASM2276707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:42:31,489] [INFO] Task succeeded: fastANI
[2023-06-13 22:42:31,499] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 22:42:31,499] [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_009695765.1	s__VUNI01 sp009695765	78.5187	97	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363675.1	s__Agathobacter sp000434275	77.7646	96	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.18	99.14	0.93	0.89	5	-
GCF_000174195.1	s__Roseburia inulinivorans	77.6106	73	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCA_003483745.1	s__Roseburia sp003483745	77.5771	64	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_900552085.1	s__Agathobacter sp900552085	77.5092	73	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_900550545.1	s__Agathobacter sp900550545	77.2174	87	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003479605.1	s__RUG115 sp900066395	77.1335	85	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	98.27	97.78	0.88	0.83	29	-
GCA_017623935.1	s__Agathobacter sp017623935	77.013	78	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.03	99.03	0.82	0.82	2	-
GCA_015057035.1	s__Agathobacter sp015057035	76.9469	69	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550935.1	s__Roseburia sp900550935	76.8998	57	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCA_900543445.1	s__Agathobacter sp900543445	76.8266	80	614	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-13 22:42:31,501] [INFO] GTDB search result was written to GCA_022767075.1_ASM2276707v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:42:31,502] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:42:31,505] [INFO] DFAST_QC result json was written to GCA_022767075.1_ASM2276707v1_genomic.fna/dqc_result.json
[2023-06-13 22:42:31,505] [INFO] DFAST_QC completed!
[2023-06-13 22:42:31,505] [INFO] Total running time: 0h0m57s