[2023-06-28 11:35:44,711] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:35:44,712] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:35:44,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b165d9e-9f36-4137-bc5e-814431c5e60a/dqc_reference
[2023-06-28 11:35:45,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:35:45,842] [INFO] Task started: Prodigal
[2023-06-28 11:35:45,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bb66268-b656-4bac-9630-2c9905d99357/GCA_017401185.1_ASM1740118v1_genomic.fna.gz | prodigal -d GCA_017401185.1_ASM1740118v1_genomic.fna/cds.fna -a GCA_017401185.1_ASM1740118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:35:48,876] [INFO] Task succeeded: Prodigal
[2023-06-28 11:35:48,876] [INFO] Task started: HMMsearch
[2023-06-28 11:35:48,876] [INFO] Running command: hmmsearch --tblout GCA_017401185.1_ASM1740118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b165d9e-9f36-4137-bc5e-814431c5e60a/dqc_reference/reference_markers.hmm GCA_017401185.1_ASM1740118v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:35:49,063] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:35:49,064] [INFO] Found 6/6 markers.
[2023-06-28 11:35:49,083] [INFO] Query marker FASTA was written to GCA_017401185.1_ASM1740118v1_genomic.fna/markers.fasta
[2023-06-28 11:35:49,083] [INFO] Task started: Blastn
[2023-06-28 11:35:49,083] [INFO] Running command: blastn -query GCA_017401185.1_ASM1740118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b165d9e-9f36-4137-bc5e-814431c5e60a/dqc_reference/reference_markers.fasta -out GCA_017401185.1_ASM1740118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:35:49,613] [INFO] Task succeeded: Blastn
[2023-06-28 11:35:49,616] [INFO] Selected 19 target genomes.
[2023-06-28 11:35:49,616] [INFO] Target genome list was writen to GCA_017401185.1_ASM1740118v1_genomic.fna/target_genomes.txt
[2023-06-28 11:35:49,623] [INFO] Task started: fastANI
[2023-06-28 11:35:49,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb66268-b656-4bac-9630-2c9905d99357/GCA_017401185.1_ASM1740118v1_genomic.fna.gz --refList GCA_017401185.1_ASM1740118v1_genomic.fna/target_genomes.txt --output GCA_017401185.1_ASM1740118v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:35:59,556] [INFO] Task succeeded: fastANI
[2023-06-28 11:35:59,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b165d9e-9f36-4137-bc5e-814431c5e60a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:35:59,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b165d9e-9f36-4137-bc5e-814431c5e60a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:35:59,560] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:35:59,560] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 11:35:59,560] [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	78.7411	178	473	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:35:59,561] [INFO] DFAST Taxonomy check result was written to GCA_017401185.1_ASM1740118v1_genomic.fna/tc_result.tsv
[2023-06-28 11:35:59,561] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:35:59,562] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:35:59,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b165d9e-9f36-4137-bc5e-814431c5e60a/dqc_reference/checkm_data
[2023-06-28 11:35:59,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:35:59,585] [INFO] Task started: CheckM
[2023-06-28 11:35:59,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017401185.1_ASM1740118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017401185.1_ASM1740118v1_genomic.fna/checkm_input GCA_017401185.1_ASM1740118v1_genomic.fna/checkm_result
[2023-06-28 11:36:14,672] [INFO] Task succeeded: CheckM
[2023-06-28 11:36:14,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 11:36:14,688] [INFO] ===== Completeness check finished =====
[2023-06-28 11:36:14,688] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:36:14,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017401185.1_ASM1740118v1_genomic.fna/markers.fasta)
[2023-06-28 11:36:14,689] [INFO] Task started: Blastn
[2023-06-28 11:36:14,689] [INFO] Running command: blastn -query GCA_017401185.1_ASM1740118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b165d9e-9f36-4137-bc5e-814431c5e60a/dqc_reference/reference_markers_gtdb.fasta -out GCA_017401185.1_ASM1740118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:36:15,510] [INFO] Task succeeded: Blastn
[2023-06-28 11:36:15,513] [INFO] Selected 11 target genomes.
[2023-06-28 11:36:15,513] [INFO] Target genome list was writen to GCA_017401185.1_ASM1740118v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:36:15,527] [INFO] Task started: fastANI
[2023-06-28 11:36:15,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb66268-b656-4bac-9630-2c9905d99357/GCA_017401185.1_ASM1740118v1_genomic.fna.gz --refList GCA_017401185.1_ASM1740118v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017401185.1_ASM1740118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:36:21,034] [INFO] Task succeeded: fastANI
[2023-06-28 11:36:21,041] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:36:21,042] [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_017543335.1	s__Ruminococcus sp017543335	98.3578	424	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.36	98.36	0.90	0.90	2	conclusive
GCA_017441505.1	s__Ruminococcus sp017441505	94.6294	381	473	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_001604035.1	s__Ruminococcus sp001604035	79.5924	193	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.76	98.76	0.77	0.77	2	-
GCA_012718885.1	s__Ruminococcus sp012718885	79.3032	199	473	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_002371825.1	s__Ruminococcus flavefaciens_L	79.2875	236	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.29	98.12	0.89	0.86	3	-
GCA_902780115.1	s__Ruminococcus flavefaciens_Y	79.0507	118	473	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_902762855.1	s__Ruminococcus flavefaciens_V	79.027	204	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.58	98.43	0.85	0.84	3	-
GCF_900108555.1	s__Ruminococcus flavefaciens_P	78.8185	184	473	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_900119075.1	s__Ruminococcus flavefaciens_Q	78.805	153	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.02	98.02	0.91	0.91	2	-
GCA_905199285.1	s__Ruminococcus sp905199285	78.158	138	473	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_017462565.1	s__Ruminococcus sp017462565	78.0568	145	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:36:21,046] [INFO] GTDB search result was written to GCA_017401185.1_ASM1740118v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:36:21,046] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:36:21,048] [INFO] DFAST_QC result json was written to GCA_017401185.1_ASM1740118v1_genomic.fna/dqc_result.json
[2023-06-28 11:36:21,049] [INFO] DFAST_QC completed!
[2023-06-28 11:36:21,049] [INFO] Total running time: 0h0m36s