[2023-06-05 02:37:47,565] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:37:47,567] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:37:47,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f705480-fe84-4e30-8a2b-3304f7e8960c/dqc_reference
[2023-06-05 02:37:48,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:37:48,957] [INFO] Task started: Prodigal
[2023-06-05 02:37:48,957] [INFO] Running command: gunzip -c /var/lib/cwl/stgdccbbc6c-e50c-4f33-b480-63474387609d/GCA_934835635.1_MTG223_bin.2.fa_genomic.fna.gz | prodigal -d GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/cds.fna -a GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:37:54,606] [INFO] Task succeeded: Prodigal
[2023-06-05 02:37:54,606] [INFO] Task started: HMMsearch
[2023-06-05 02:37:54,606] [INFO] Running command: hmmsearch --tblout GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f705480-fe84-4e30-8a2b-3304f7e8960c/dqc_reference/reference_markers.hmm GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:37:54,777] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:37:54,778] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdccbbc6c-e50c-4f33-b480-63474387609d/GCA_934835635.1_MTG223_bin.2.fa_genomic.fna.gz]
[2023-06-05 02:37:54,802] [INFO] Query marker FASTA was written to GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/markers.fasta
[2023-06-05 02:37:54,802] [INFO] Task started: Blastn
[2023-06-05 02:37:54,802] [INFO] Running command: blastn -query GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f705480-fe84-4e30-8a2b-3304f7e8960c/dqc_reference/reference_markers.fasta -out GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:37:55,356] [INFO] Task succeeded: Blastn
[2023-06-05 02:37:55,360] [INFO] Selected 22 target genomes.
[2023-06-05 02:37:55,360] [INFO] Target genome list was writen to GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/target_genomes.txt
[2023-06-05 02:37:55,366] [INFO] Task started: fastANI
[2023-06-05 02:37:55,366] [INFO] Running command: fastANI --query /var/lib/cwl/stgdccbbc6c-e50c-4f33-b480-63474387609d/GCA_934835635.1_MTG223_bin.2.fa_genomic.fna.gz --refList GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/target_genomes.txt --output GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:38:07,919] [INFO] Task succeeded: fastANI
[2023-06-05 02:38:07,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f705480-fe84-4e30-8a2b-3304f7e8960c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:38:07,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f705480-fe84-4e30-8a2b-3304f7e8960c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:38:07,924] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:38:07,924] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:38:07,924] [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
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	77.1644	64	733	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.9731	63	733	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.7782	57	733	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:38:07,926] [INFO] DFAST Taxonomy check result was written to GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/tc_result.tsv
[2023-06-05 02:38:07,926] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:38:07,927] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:38:07,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f705480-fe84-4e30-8a2b-3304f7e8960c/dqc_reference/checkm_data
[2023-06-05 02:38:07,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:38:07,954] [INFO] Task started: CheckM
[2023-06-05 02:38:07,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/checkm_input GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/checkm_result
[2023-06-05 02:38:31,387] [INFO] Task succeeded: CheckM
[2023-06-05 02:38:31,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:38:31,405] [INFO] ===== Completeness check finished =====
[2023-06-05 02:38:31,405] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:38:31,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/markers.fasta)
[2023-06-05 02:38:31,406] [INFO] Task started: Blastn
[2023-06-05 02:38:31,406] [INFO] Running command: blastn -query GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f705480-fe84-4e30-8a2b-3304f7e8960c/dqc_reference/reference_markers_gtdb.fasta -out GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:38:32,168] [INFO] Task succeeded: Blastn
[2023-06-05 02:38:32,171] [INFO] Selected 7 target genomes.
[2023-06-05 02:38:32,171] [INFO] Target genome list was writen to GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:38:32,176] [INFO] Task started: fastANI
[2023-06-05 02:38:32,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgdccbbc6c-e50c-4f33-b480-63474387609d/GCA_934835635.1_MTG223_bin.2.fa_genomic.fna.gz --refList GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:38:36,559] [INFO] Task succeeded: fastANI
[2023-06-05 02:38:36,567] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:38:36,567] [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_009695995.1	s__Acetatifactor intestinalis	97.0555	615	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	96.98	96.46	0.81	0.76	18	conclusive
GCA_003447295.1	s__Acetatifactor sp003447295	92.5671	478	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	97.04	96.84	0.74	0.71	4	-
GCA_003584705.1	s__Acetatifactor sp900066565	89.2572	604	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.01	97.56	0.88	0.80	26	-
GCA_900772845.1	s__Acetatifactor sp900772845	88.1456	547	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	95.92	95.92	0.80	0.80	2	-
GCA_002431915.1	s__Acetatifactor sp002431915	87.5502	540	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900771995.1	s__Acetatifactor sp900771995	86.8957	541	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766575.1	s__Acetatifactor sp900766575	85.4985	382	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:38:36,569] [INFO] GTDB search result was written to GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 02:38:36,569] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:38:36,572] [INFO] DFAST_QC result json was written to GCA_934835635.1_MTG223_bin.2.fa_genomic.fna/dqc_result.json
[2023-06-05 02:38:36,572] [INFO] DFAST_QC completed!
[2023-06-05 02:38:36,572] [INFO] Total running time: 0h0m49s