[2023-06-29 12:49:24,149] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:49:24,151] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:49:24,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg163e29b2-5b30-4cf2-9cbc-d7801f9f4949/dqc_reference
[2023-06-29 12:49:25,431] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:49:25,432] [INFO] Task started: Prodigal
[2023-06-29 12:49:25,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg40df8715-67af-4b97-8dc7-cfa7177a350c/GCA_023404295.1_ASM2340429v1_genomic.fna.gz | prodigal -d GCA_023404295.1_ASM2340429v1_genomic.fna/cds.fna -a GCA_023404295.1_ASM2340429v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:49:32,926] [INFO] Task succeeded: Prodigal
[2023-06-29 12:49:32,927] [INFO] Task started: HMMsearch
[2023-06-29 12:49:32,927] [INFO] Running command: hmmsearch --tblout GCA_023404295.1_ASM2340429v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg163e29b2-5b30-4cf2-9cbc-d7801f9f4949/dqc_reference/reference_markers.hmm GCA_023404295.1_ASM2340429v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:49:33,220] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:49:33,221] [INFO] Found 6/6 markers.
[2023-06-29 12:49:33,261] [INFO] Query marker FASTA was written to GCA_023404295.1_ASM2340429v1_genomic.fna/markers.fasta
[2023-06-29 12:49:33,262] [INFO] Task started: Blastn
[2023-06-29 12:49:33,262] [INFO] Running command: blastn -query GCA_023404295.1_ASM2340429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg163e29b2-5b30-4cf2-9cbc-d7801f9f4949/dqc_reference/reference_markers.fasta -out GCA_023404295.1_ASM2340429v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:49:33,884] [INFO] Task succeeded: Blastn
[2023-06-29 12:49:33,889] [INFO] Selected 18 target genomes.
[2023-06-29 12:49:33,890] [INFO] Target genome list was writen to GCA_023404295.1_ASM2340429v1_genomic.fna/target_genomes.txt
[2023-06-29 12:49:33,895] [INFO] Task started: fastANI
[2023-06-29 12:49:33,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg40df8715-67af-4b97-8dc7-cfa7177a350c/GCA_023404295.1_ASM2340429v1_genomic.fna.gz --refList GCA_023404295.1_ASM2340429v1_genomic.fna/target_genomes.txt --output GCA_023404295.1_ASM2340429v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:49:43,485] [INFO] Task succeeded: fastANI
[2023-06-29 12:49:43,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg163e29b2-5b30-4cf2-9cbc-d7801f9f4949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:49:43,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg163e29b2-5b30-4cf2-9cbc-d7801f9f4949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:49:43,492] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 12:49:43,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 12:49:43,492] [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	97.367	1256	1477	95	conclusive
Cellulosilyticum ruminicola	strain=JCM 14822	GCA_001311925.1	425254	425254	type	True	78.5798	286	1477	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:49:43,495] [INFO] DFAST Taxonomy check result was written to GCA_023404295.1_ASM2340429v1_genomic.fna/tc_result.tsv
[2023-06-29 12:49:43,495] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:49:43,496] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:49:43,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg163e29b2-5b30-4cf2-9cbc-d7801f9f4949/dqc_reference/checkm_data
[2023-06-29 12:49:43,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:49:43,547] [INFO] Task started: CheckM
[2023-06-29 12:49:43,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023404295.1_ASM2340429v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023404295.1_ASM2340429v1_genomic.fna/checkm_input GCA_023404295.1_ASM2340429v1_genomic.fna/checkm_result
[2023-06-29 12:50:12,240] [INFO] Task succeeded: CheckM
[2023-06-29 12:50:12,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:50:12,262] [INFO] ===== Completeness check finished =====
[2023-06-29 12:50:12,262] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:50:12,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023404295.1_ASM2340429v1_genomic.fna/markers.fasta)
[2023-06-29 12:50:12,263] [INFO] Task started: Blastn
[2023-06-29 12:50:12,263] [INFO] Running command: blastn -query GCA_023404295.1_ASM2340429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg163e29b2-5b30-4cf2-9cbc-d7801f9f4949/dqc_reference/reference_markers_gtdb.fasta -out GCA_023404295.1_ASM2340429v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:50:13,236] [INFO] Task succeeded: Blastn
[2023-06-29 12:50:13,241] [INFO] Selected 15 target genomes.
[2023-06-29 12:50:13,241] [INFO] Target genome list was writen to GCA_023404295.1_ASM2340429v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:50:13,245] [INFO] Task started: fastANI
[2023-06-29 12:50:13,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg40df8715-67af-4b97-8dc7-cfa7177a350c/GCA_023404295.1_ASM2340429v1_genomic.fna.gz --refList GCA_023404295.1_ASM2340429v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023404295.1_ASM2340429v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:50:21,700] [INFO] Task succeeded: fastANI
[2023-06-29 12:50:21,712] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:50:21,713] [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	97.367	1256	1477	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_018883705.1	s__Cellulosilyticum pullistercoris	79.2819	263	1477	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_017941635.1	s__Cellulosilyticum sp017941635	79.0983	284	1477	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	78.6168	226	1477	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	78.5902	284	1477	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	78.5597	338	1477	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	78.5327	159	1477	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_900551325.1	s__Niameybacter sp900551325	77.5874	178	1477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384995.1	s__Niameybacter stercoravium	77.5603	167	1477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	97.76	95.05	0.90	0.86	8	-
--------------------------------------------------------------------------------
[2023-06-29 12:50:21,715] [INFO] GTDB search result was written to GCA_023404295.1_ASM2340429v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:50:21,715] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:50:21,730] [INFO] DFAST_QC result json was written to GCA_023404295.1_ASM2340429v1_genomic.fna/dqc_result.json
[2023-06-29 12:50:21,730] [INFO] DFAST_QC completed!
[2023-06-29 12:50:21,730] [INFO] Total running time: 0h0m58s