[2023-06-05 10:46:37,607] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:46:37,609] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:46:37,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgb20e2c74-6135-4334-a9a0-8882651d4ffc/dqc_reference
[2023-06-05 10:46:41,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:46:41,146] [INFO] Task started: Prodigal
[2023-06-05 10:46:41,147] [INFO] Running command: gunzip -c /var/lib/cwl/stgc974c457-4118-49aa-afbb-200187478e48/GCA_902836435.1_MGYG-HGUT-04685_genomic.fna.gz | prodigal -d GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/cds.fna -a GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:46:44,384] [INFO] Task succeeded: Prodigal
[2023-06-05 10:46:44,385] [INFO] Task started: HMMsearch
[2023-06-05 10:46:44,385] [INFO] Running command: hmmsearch --tblout GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb20e2c74-6135-4334-a9a0-8882651d4ffc/dqc_reference/reference_markers.hmm GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:46:44,601] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:46:44,602] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc974c457-4118-49aa-afbb-200187478e48/GCA_902836435.1_MGYG-HGUT-04685_genomic.fna.gz]
[2023-06-05 10:46:44,626] [INFO] Query marker FASTA was written to GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/markers.fasta
[2023-06-05 10:46:44,627] [INFO] Task started: Blastn
[2023-06-05 10:46:44,627] [INFO] Running command: blastn -query GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/markers.fasta -db /var/lib/cwl/stgb20e2c74-6135-4334-a9a0-8882651d4ffc/dqc_reference/reference_markers.fasta -out GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:46:46,337] [INFO] Task succeeded: Blastn
[2023-06-05 10:46:46,341] [INFO] Selected 13 target genomes.
[2023-06-05 10:46:46,342] [INFO] Target genome list was writen to GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/target_genomes.txt
[2023-06-05 10:46:46,345] [INFO] Task started: fastANI
[2023-06-05 10:46:46,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgc974c457-4118-49aa-afbb-200187478e48/GCA_902836435.1_MGYG-HGUT-04685_genomic.fna.gz --refList GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/target_genomes.txt --output GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:46:50,727] [INFO] Task succeeded: fastANI
[2023-06-05 10:46:50,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb20e2c74-6135-4334-a9a0-8882651d4ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:46:50,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb20e2c74-6135-4334-a9a0-8882651d4ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:46:50,737] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:46:50,738] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:46:50,738] [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
Holdemanella porci	strain=LKV-472-APC-3	GCA_009696075.1	2652276	2652276	suspected-type	True	94.4869	89	134	95	below_threshold
Holdemanella biformis	strain=DSM 3989	GCA_000156655.1	1735	1735	suspected-type	True	92.2863	96	134	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:46:50,741] [INFO] DFAST Taxonomy check result was written to GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/tc_result.tsv
[2023-06-05 10:46:50,741] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:46:50,741] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:46:50,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb20e2c74-6135-4334-a9a0-8882651d4ffc/dqc_reference/checkm_data
[2023-06-05 10:46:50,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:46:50,769] [INFO] Task started: CheckM
[2023-06-05 10:46:50,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/checkm_input GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/checkm_result
[2023-06-05 10:47:09,652] [INFO] Task succeeded: CheckM
[2023-06-05 10:47:09,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.54%
Contamintation: 5.82%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:47:09,676] [INFO] ===== Completeness check finished =====
[2023-06-05 10:47:09,677] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:47:09,677] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/markers.fasta)
[2023-06-05 10:47:09,677] [INFO] Task started: Blastn
[2023-06-05 10:47:09,677] [INFO] Running command: blastn -query GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/markers.fasta -db /var/lib/cwl/stgb20e2c74-6135-4334-a9a0-8882651d4ffc/dqc_reference/reference_markers_gtdb.fasta -out GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:10,661] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:10,666] [INFO] Selected 8 target genomes.
[2023-06-05 10:47:10,666] [INFO] Target genome list was writen to GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:47:10,673] [INFO] Task started: fastANI
[2023-06-05 10:47:10,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgc974c457-4118-49aa-afbb-200187478e48/GCA_902836435.1_MGYG-HGUT-04685_genomic.fna.gz --refList GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/target_genomes_gtdb.txt --output GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:47:13,159] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:13,168] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:47:13,168] [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_003458715.1	s__Holdemanella sp003458715	95.5845	98	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.81	97.17	0.85	0.77	7	conclusive
GCF_009696075.1	s__Holdemanella porci	94.4869	89	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.44	95.01	0.80	0.66	21	-
GCF_003436425.1	s__Holdemanella sp003436425	92.5333	100	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	98.46	97.77	0.88	0.82	5	-
GCA_900556915.1	s__Holdemanella sp900556915	92.5295	80	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.25	96.18	0.85	0.83	3	-
GCF_000156655.1	s__Holdemanella biformis	92.2863	96	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.82	95.86	0.79	0.56	17	-
GCA_900547815.1	s__Holdemanella sp900547815	92.2082	89	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.44	96.94	0.79	0.75	3	-
GCA_900754615.1	s__Holdemanella sp900754615	91.9968	90	134	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:47:13,171] [INFO] GTDB search result was written to GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/result_gtdb.tsv
[2023-06-05 10:47:13,171] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:47:13,174] [INFO] DFAST_QC result json was written to GCA_902836435.1_MGYG-HGUT-04685_genomic.fna/dqc_result.json
[2023-06-05 10:47:13,175] [INFO] DFAST_QC completed!
[2023-06-05 10:47:13,175] [INFO] Total running time: 0h0m36s