[2024-01-25 18:28:50,578] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:50,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:50,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg54871cb1-49ec-429d-96b3-5e61364ad03c/dqc_reference
[2024-01-25 18:28:51,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:51,670] [INFO] Task started: Prodigal
[2024-01-25 18:28:51,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg76648f2b-4545-4f50-adfb-5b3b61a432b8/GCF_000178835.2_ASM17883v2_genomic.fna.gz | prodigal -d GCF_000178835.2_ASM17883v2_genomic.fna/cds.fna -a GCF_000178835.2_ASM17883v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:28:58,903] [INFO] Task succeeded: Prodigal
[2024-01-25 18:28:58,903] [INFO] Task started: HMMsearch
[2024-01-25 18:28:58,903] [INFO] Running command: hmmsearch --tblout GCF_000178835.2_ASM17883v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54871cb1-49ec-429d-96b3-5e61364ad03c/dqc_reference/reference_markers.hmm GCF_000178835.2_ASM17883v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:28:59,135] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:28:59,136] [INFO] Found 6/6 markers.
[2024-01-25 18:28:59,173] [INFO] Query marker FASTA was written to GCF_000178835.2_ASM17883v2_genomic.fna/markers.fasta
[2024-01-25 18:28:59,174] [INFO] Task started: Blastn
[2024-01-25 18:28:59,174] [INFO] Running command: blastn -query GCF_000178835.2_ASM17883v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg54871cb1-49ec-429d-96b3-5e61364ad03c/dqc_reference/reference_markers.fasta -out GCF_000178835.2_ASM17883v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:28:59,741] [INFO] Task succeeded: Blastn
[2024-01-25 18:28:59,744] [INFO] Selected 18 target genomes.
[2024-01-25 18:28:59,744] [INFO] Target genome list was writen to GCF_000178835.2_ASM17883v2_genomic.fna/target_genomes.txt
[2024-01-25 18:28:59,770] [INFO] Task started: fastANI
[2024-01-25 18:28:59,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg76648f2b-4545-4f50-adfb-5b3b61a432b8/GCF_000178835.2_ASM17883v2_genomic.fna.gz --refList GCF_000178835.2_ASM17883v2_genomic.fna/target_genomes.txt --output GCF_000178835.2_ASM17883v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:29:09,863] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:09,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54871cb1-49ec-429d-96b3-5e61364ad03c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:29:09,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54871cb1-49ec-429d-96b3-5e61364ad03c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:29:09,868] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:29:09,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:29:09,868] [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
Cellulosilyticum lentocellum	strain=DSM 5427	GCA_000178835.2	29360	29360	type	True	100.0	1571	1571	95	conclusive
Cellulosilyticum ruminicola	strain=JCM 14822	GCA_001311925.1	425254	425254	type	True	79.0186	292	1571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:29:09,869] [INFO] DFAST Taxonomy check result was written to GCF_000178835.2_ASM17883v2_genomic.fna/tc_result.tsv
[2024-01-25 18:29:09,870] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:29:09,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:29:09,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54871cb1-49ec-429d-96b3-5e61364ad03c/dqc_reference/checkm_data
[2024-01-25 18:29:09,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:29:09,919] [INFO] Task started: CheckM
[2024-01-25 18:29:09,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000178835.2_ASM17883v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000178835.2_ASM17883v2_genomic.fna/checkm_input GCF_000178835.2_ASM17883v2_genomic.fna/checkm_result
[2024-01-25 18:29:36,087] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:36,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:36,123] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:36,123] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:36,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000178835.2_ASM17883v2_genomic.fna/markers.fasta)
[2024-01-25 18:29:36,124] [INFO] Task started: Blastn
[2024-01-25 18:29:36,124] [INFO] Running command: blastn -query GCF_000178835.2_ASM17883v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg54871cb1-49ec-429d-96b3-5e61364ad03c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000178835.2_ASM17883v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:37,133] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:37,136] [INFO] Selected 15 target genomes.
[2024-01-25 18:29:37,136] [INFO] Target genome list was writen to GCF_000178835.2_ASM17883v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:37,146] [INFO] Task started: fastANI
[2024-01-25 18:29:37,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg76648f2b-4545-4f50-adfb-5b3b61a432b8/GCF_000178835.2_ASM17883v2_genomic.fna.gz --refList GCF_000178835.2_ASM17883v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000178835.2_ASM17883v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:29:46,718] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:46,725] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:29:46,726] [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_000178835.2	s__Cellulosilyticum lentocellum	100.0	1571	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	97.43	97.43	0.84	0.84	2	conclusive
GCA_017941635.1	s__Cellulosilyticum sp017941635	79.2186	300	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883705.1	s__Cellulosilyticum pullistercoris	79.0829	278	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311925.1	s__Cellulosilyticum ruminicola	79.0286	289	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058045.1	s__Cellulosilyticum sp015058045	78.9239	345	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017421915.1	s__Cellulosilyticum sp017421915	78.6784	229	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556665.1	s__Cellulosilyticum sp900556665	78.2504	171	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384995.1	s__Niameybacter stercoravium	78.0306	180	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	97.76	95.05	0.90	0.86	8	-
GCA_900551325.1	s__Niameybacter sp900551325	77.87	182	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095725.1	s__FMMP01 sp900095725	77.4061	173	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__FMMP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001466305.1	s__Defluviitalea phaphyphila	76.0304	65	1571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:29:46,727] [INFO] GTDB search result was written to GCF_000178835.2_ASM17883v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:29:46,728] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:29:46,730] [INFO] DFAST_QC result json was written to GCF_000178835.2_ASM17883v2_genomic.fna/dqc_result.json
[2024-01-25 18:29:46,730] [INFO] DFAST_QC completed!
[2024-01-25 18:29:46,731] [INFO] Total running time: 0h0m56s