[2023-06-28 10:22:07,841] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:22:07,847] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:22:07,847] [INFO] DQC Reference Directory: /var/lib/cwl/stgaac3b381-7467-4305-9305-aafeea2f990d/dqc_reference
[2023-06-28 10:22:10,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:22:10,422] [INFO] Task started: Prodigal
[2023-06-28 10:22:10,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fb18039-b3c9-4e15-afc0-e6e6670dba42/GCA_944385705.1_BRZ_NQ_bin25_genomic.fna.gz | prodigal -d GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/cds.fna -a GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:22:16,531] [INFO] Task succeeded: Prodigal
[2023-06-28 10:22:16,531] [INFO] Task started: HMMsearch
[2023-06-28 10:22:16,532] [INFO] Running command: hmmsearch --tblout GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaac3b381-7467-4305-9305-aafeea2f990d/dqc_reference/reference_markers.hmm GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:22:16,819] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:22:16,820] [INFO] Found 6/6 markers.
[2023-06-28 10:22:16,850] [INFO] Query marker FASTA was written to GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/markers.fasta
[2023-06-28 10:22:16,851] [INFO] Task started: Blastn
[2023-06-28 10:22:16,851] [INFO] Running command: blastn -query GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/markers.fasta -db /var/lib/cwl/stgaac3b381-7467-4305-9305-aafeea2f990d/dqc_reference/reference_markers.fasta -out GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:22:17,524] [INFO] Task succeeded: Blastn
[2023-06-28 10:22:17,528] [INFO] Selected 14 target genomes.
[2023-06-28 10:22:17,529] [INFO] Target genome list was writen to GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/target_genomes.txt
[2023-06-28 10:22:17,531] [INFO] Task started: fastANI
[2023-06-28 10:22:17,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fb18039-b3c9-4e15-afc0-e6e6670dba42/GCA_944385705.1_BRZ_NQ_bin25_genomic.fna.gz --refList GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/target_genomes.txt --output GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:22:24,936] [INFO] Task succeeded: fastANI
[2023-06-28 10:22:24,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaac3b381-7467-4305-9305-aafeea2f990d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:22:24,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaac3b381-7467-4305-9305-aafeea2f990d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:22:24,954] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:22:24,955] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:22:24,955] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.2146	107	702	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.1752	69	702	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.9552	96	702	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	76.7925	69	702	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.5812	61	702	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.547	62	702	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	76.4435	63	702	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:22:24,957] [INFO] DFAST Taxonomy check result was written to GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/tc_result.tsv
[2023-06-28 10:22:24,958] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:22:24,958] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:22:24,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaac3b381-7467-4305-9305-aafeea2f990d/dqc_reference/checkm_data
[2023-06-28 10:22:24,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:22:24,997] [INFO] Task started: CheckM
[2023-06-28 10:22:24,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/checkm_input GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/checkm_result
[2023-06-28 10:22:50,079] [INFO] Task succeeded: CheckM
[2023-06-28 10:22:50,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:22:50,103] [INFO] ===== Completeness check finished =====
[2023-06-28 10:22:50,103] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:22:50,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/markers.fasta)
[2023-06-28 10:22:50,104] [INFO] Task started: Blastn
[2023-06-28 10:22:50,104] [INFO] Running command: blastn -query GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/markers.fasta -db /var/lib/cwl/stgaac3b381-7467-4305-9305-aafeea2f990d/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:22:51,035] [INFO] Task succeeded: Blastn
[2023-06-28 10:22:51,040] [INFO] Selected 19 target genomes.
[2023-06-28 10:22:51,041] [INFO] Target genome list was writen to GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:22:51,049] [INFO] Task started: fastANI
[2023-06-28 10:22:51,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fb18039-b3c9-4e15-afc0-e6e6670dba42/GCA_944385705.1_BRZ_NQ_bin25_genomic.fna.gz --refList GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/target_genomes_gtdb.txt --output GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:22:59,209] [INFO] Task succeeded: fastANI
[2023-06-28 10:22:59,228] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:22:59,228] [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_018711755.1	s__Limivicinus faecipullorum	87.624	434	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754515.1	s__Limivicinus sp900754515	85.9965	519	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.83	97.83	0.85	0.85	2	-
GCA_004560305.1	s__Limivicinus sp004560305	81.868	302	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	96.68	96.68	0.69	0.69	2	-
GCA_902787755.1	s__Limivicinus sp902787755	79.3606	188	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319635.1	s__Limivicinus sp900319635	79.3497	188	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.84	96.83	0.85	0.76	6	-
GCA_017470325.1	s__Limivicinus sp017470325	79.3224	200	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765595.1	s__Limivicinus sp002350825	79.294	195	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.80	99.80	0.90	0.90	2	-
GCA_017545165.1	s__Limivicinus sp017545165	79.2868	156	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458085.1	s__Limivicinus sp017458085	79.1553	179	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775355.1	s__Limivicinus sp902775355	79.0621	214	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428565.1	s__Limivicinus sp017428565	79.0507	198	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778275.1	s__Limivicinus sp902778275	78.8845	220	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320035.1	s__Limivicinus sp002320035	78.837	166	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.95	98.71	0.80	0.75	5	-
GCA_902791215.1	s__Limivicinus sp902791215	78.7094	195	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003150355.1	s__Limivicinus sp003150355	78.5184	138	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.34	96.94	0.74	0.68	6	-
GCA_902793285.1	s__Limivicinus sp902793285	78.5163	169	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.34	97.34	0.78	0.78	2	-
GCA_902779945.1	s__Limivicinus sp902779945	78.4353	168	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410425.1	s__Limivicinus sp017410425	78.2467	150	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789745.1	s__Limivicinus sp902789745	77.652	148	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:22:59,231] [INFO] GTDB search result was written to GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/result_gtdb.tsv
[2023-06-28 10:22:59,233] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:22:59,236] [INFO] DFAST_QC result json was written to GCA_944385705.1_BRZ_NQ_bin25_genomic.fna/dqc_result.json
[2023-06-28 10:22:59,236] [INFO] DFAST_QC completed!
[2023-06-28 10:22:59,236] [INFO] Total running time: 0h0m51s