[2023-06-29 17:18:32,120] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:18:32,122] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:18:32,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ce1e623-9dd8-49db-9ec2-f3afe3dcd292/dqc_reference
[2023-06-29 17:18:33,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:18:33,318] [INFO] Task started: Prodigal
[2023-06-29 17:18:33,318] [INFO] Running command: gunzip -c /var/lib/cwl/stgf244e22a-6a5d-4e52-be99-a6e8002d7299/GCA_910580145.1_MGBC120617_genomic.fna.gz | prodigal -d GCA_910580145.1_MGBC120617_genomic.fna/cds.fna -a GCA_910580145.1_MGBC120617_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:18:38,565] [INFO] Task succeeded: Prodigal
[2023-06-29 17:18:38,565] [INFO] Task started: HMMsearch
[2023-06-29 17:18:38,566] [INFO] Running command: hmmsearch --tblout GCA_910580145.1_MGBC120617_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ce1e623-9dd8-49db-9ec2-f3afe3dcd292/dqc_reference/reference_markers.hmm GCA_910580145.1_MGBC120617_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:18:38,769] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:18:38,770] [INFO] Found 6/6 markers.
[2023-06-29 17:18:38,792] [INFO] Query marker FASTA was written to GCA_910580145.1_MGBC120617_genomic.fna/markers.fasta
[2023-06-29 17:18:38,793] [INFO] Task started: Blastn
[2023-06-29 17:18:38,793] [INFO] Running command: blastn -query GCA_910580145.1_MGBC120617_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ce1e623-9dd8-49db-9ec2-f3afe3dcd292/dqc_reference/reference_markers.fasta -out GCA_910580145.1_MGBC120617_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:18:39,405] [INFO] Task succeeded: Blastn
[2023-06-29 17:18:39,408] [INFO] Selected 25 target genomes.
[2023-06-29 17:18:39,408] [INFO] Target genome list was writen to GCA_910580145.1_MGBC120617_genomic.fna/target_genomes.txt
[2023-06-29 17:18:39,411] [INFO] Task started: fastANI
[2023-06-29 17:18:39,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgf244e22a-6a5d-4e52-be99-a6e8002d7299/GCA_910580145.1_MGBC120617_genomic.fna.gz --refList GCA_910580145.1_MGBC120617_genomic.fna/target_genomes.txt --output GCA_910580145.1_MGBC120617_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:18:50,754] [INFO] Task succeeded: fastANI
[2023-06-29 17:18:50,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ce1e623-9dd8-49db-9ec2-f3afe3dcd292/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:18:50,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ce1e623-9dd8-49db-9ec2-f3afe3dcd292/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:18:50,758] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:18:50,759] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 17:18:50,759] [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
Ruminococcus flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	78.1559	143	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 17:18:50,779] [INFO] DFAST Taxonomy check result was written to GCA_910580145.1_MGBC120617_genomic.fna/tc_result.tsv
[2023-06-29 17:18:50,780] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:18:50,780] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:18:50,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ce1e623-9dd8-49db-9ec2-f3afe3dcd292/dqc_reference/checkm_data
[2023-06-29 17:18:50,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:18:50,806] [INFO] Task started: CheckM
[2023-06-29 17:18:50,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910580145.1_MGBC120617_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910580145.1_MGBC120617_genomic.fna/checkm_input GCA_910580145.1_MGBC120617_genomic.fna/checkm_result
[2023-06-29 17:19:12,662] [INFO] Task succeeded: CheckM
[2023-06-29 17:19:12,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:19:12,679] [INFO] ===== Completeness check finished =====
[2023-06-29 17:19:12,680] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:19:12,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910580145.1_MGBC120617_genomic.fna/markers.fasta)
[2023-06-29 17:19:12,680] [INFO] Task started: Blastn
[2023-06-29 17:19:12,680] [INFO] Running command: blastn -query GCA_910580145.1_MGBC120617_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ce1e623-9dd8-49db-9ec2-f3afe3dcd292/dqc_reference/reference_markers_gtdb.fasta -out GCA_910580145.1_MGBC120617_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:19:13,767] [INFO] Task succeeded: Blastn
[2023-06-29 17:19:13,771] [INFO] Selected 15 target genomes.
[2023-06-29 17:19:13,771] [INFO] Target genome list was writen to GCA_910580145.1_MGBC120617_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:19:13,777] [INFO] Task started: fastANI
[2023-06-29 17:19:13,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgf244e22a-6a5d-4e52-be99-a6e8002d7299/GCA_910580145.1_MGBC120617_genomic.fna.gz --refList GCA_910580145.1_MGBC120617_genomic.fna/target_genomes_gtdb.txt --output GCA_910580145.1_MGBC120617_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:19:21,091] [INFO] Task succeeded: fastANI
[2023-06-29 17:19:21,104] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 17:19:21,104] [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
GCA_002362135.1	s__Ruminococcus sp002362135	95.7683	515	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.94	96.10	0.89	0.86	3	conclusive
GCA_910576995.1	s__Ruminococcus sp910576995	86.707	653	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584195.1	s__Ruminococcus sp910584195	79.5165	252	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624895.1	s__Ruminococcus sp017624895	79.2029	146	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017397925.1	s__Ruminococcus sp017397925	79.1197	152	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622925.1	s__Ruminococcus sp017622925	78.9112	256	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461395.1	s__Ruminococcus sp017461395	78.6385	142	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437285.1	s__Ruminococcus sp017437285	78.4155	197	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761275.1	s__Ruminococcus sp900761275	78.4136	206	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315975.1	s__Ruminococcus sp900315975	78.3544	152	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.69	98.22	0.89	0.77	8	-
GCA_900315755.1	s__Ruminococcus sp900315755	78.2731	127	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.83	98.23	0.88	0.82	4	-
GCA_910579835.1	s__Ruminococcus sp910579835	78.1905	142	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521805.1	s__Ruminococcus sp017521805	78.1675	195	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119535.1	s__Ruminococcus flavefaciens_H	78.1182	150	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.32	96.59	0.86	0.74	4	-
GCA_017517145.1	s__Ruminococcus sp017517145	77.8551	149	808	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 17:19:21,106] [INFO] GTDB search result was written to GCA_910580145.1_MGBC120617_genomic.fna/result_gtdb.tsv
[2023-06-29 17:19:21,106] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:19:21,109] [INFO] DFAST_QC result json was written to GCA_910580145.1_MGBC120617_genomic.fna/dqc_result.json
[2023-06-29 17:19:21,109] [INFO] DFAST_QC completed!
[2023-06-29 17:19:21,109] [INFO] Total running time: 0h0m49s