[2024-01-24 12:40:50,674] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:50,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:50,676] [INFO] DQC Reference Directory: /var/lib/cwl/stge823a309-256f-4cb8-93ed-f1a340b679b4/dqc_reference
[2024-01-24 12:40:51,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:51,896] [INFO] Task started: Prodigal
[2024-01-24 12:40:51,896] [INFO] Running command: gunzip -c /var/lib/cwl/stga07ad0a4-382e-474d-a2ce-f0bd674aa5b3/GCF_900048895.1_PRJEB12697_genomic.fna.gz | prodigal -d GCF_900048895.1_PRJEB12697_genomic.fna/cds.fna -a GCF_900048895.1_PRJEB12697_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:41:01,993] [INFO] Task succeeded: Prodigal
[2024-01-24 12:41:01,993] [INFO] Task started: HMMsearch
[2024-01-24 12:41:01,993] [INFO] Running command: hmmsearch --tblout GCF_900048895.1_PRJEB12697_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge823a309-256f-4cb8-93ed-f1a340b679b4/dqc_reference/reference_markers.hmm GCF_900048895.1_PRJEB12697_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:41:02,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:41:02,252] [INFO] Found 6/6 markers.
[2024-01-24 12:41:02,286] [INFO] Query marker FASTA was written to GCF_900048895.1_PRJEB12697_genomic.fna/markers.fasta
[2024-01-24 12:41:02,287] [INFO] Task started: Blastn
[2024-01-24 12:41:02,287] [INFO] Running command: blastn -query GCF_900048895.1_PRJEB12697_genomic.fna/markers.fasta -db /var/lib/cwl/stge823a309-256f-4cb8-93ed-f1a340b679b4/dqc_reference/reference_markers.fasta -out GCF_900048895.1_PRJEB12697_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:02,943] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:02,947] [INFO] Selected 24 target genomes.
[2024-01-24 12:41:02,948] [INFO] Target genome list was writen to GCF_900048895.1_PRJEB12697_genomic.fna/target_genomes.txt
[2024-01-24 12:41:02,957] [INFO] Task started: fastANI
[2024-01-24 12:41:02,958] [INFO] Running command: fastANI --query /var/lib/cwl/stga07ad0a4-382e-474d-a2ce-f0bd674aa5b3/GCF_900048895.1_PRJEB12697_genomic.fna.gz --refList GCF_900048895.1_PRJEB12697_genomic.fna/target_genomes.txt --output GCF_900048895.1_PRJEB12697_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:15,507] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:15,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge823a309-256f-4cb8-93ed-f1a340b679b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:15,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge823a309-256f-4cb8-93ed-f1a340b679b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:15,512] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:41:15,512] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:15,513] [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
Neglectibacter timonensis	strain=SN17	GCA_900048895.1	1776382	1776382	type	True	100.0	1215	1219	95	conclusive
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.9308	65	1219	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.0991	52	1219	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:15,514] [INFO] DFAST Taxonomy check result was written to GCF_900048895.1_PRJEB12697_genomic.fna/tc_result.tsv
[2024-01-24 12:41:15,515] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:15,515] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:15,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge823a309-256f-4cb8-93ed-f1a340b679b4/dqc_reference/checkm_data
[2024-01-24 12:41:15,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:15,557] [INFO] Task started: CheckM
[2024-01-24 12:41:15,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900048895.1_PRJEB12697_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900048895.1_PRJEB12697_genomic.fna/checkm_input GCF_900048895.1_PRJEB12697_genomic.fna/checkm_result
[2024-01-24 12:41:48,832] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:48,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:48,858] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:48,858] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:48,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900048895.1_PRJEB12697_genomic.fna/markers.fasta)
[2024-01-24 12:41:48,859] [INFO] Task started: Blastn
[2024-01-24 12:41:48,859] [INFO] Running command: blastn -query GCF_900048895.1_PRJEB12697_genomic.fna/markers.fasta -db /var/lib/cwl/stge823a309-256f-4cb8-93ed-f1a340b679b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900048895.1_PRJEB12697_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:49,973] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:49,977] [INFO] Selected 20 target genomes.
[2024-01-24 12:41:49,978] [INFO] Target genome list was writen to GCF_900048895.1_PRJEB12697_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:50,063] [INFO] Task started: fastANI
[2024-01-24 12:41:50,064] [INFO] Running command: fastANI --query /var/lib/cwl/stga07ad0a4-382e-474d-a2ce-f0bd674aa5b3/GCF_900048895.1_PRJEB12697_genomic.fna.gz --refList GCF_900048895.1_PRJEB12697_genomic.fna/target_genomes_gtdb.txt --output GCF_900048895.1_PRJEB12697_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:58,827] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:58,841] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:58,841] [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_900048895.1	s__Acutalibacter timonensis	100.0	1215	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	99.93	99.87	0.99	0.98	3	conclusive
GCF_004345265.1	s__Fournierella massiliensis	78.9658	64	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	99.99	99.99	1.00	1.00	3	-
GCA_000435395.1	s__Acutalibacter ornithocaccae	77.9468	162	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	97.90	97.28	0.83	0.80	5	-
GCA_904419785.1	s__Acutalibacter sp904419785	77.8237	146	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432995.1	s__Acutalibacter sp000432995	77.6462	164	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	97.39	97.36	0.87	0.86	3	-
GCA_900543305.1	s__Acutalibacter sp900543305	77.4922	148	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215055.1	s__Acutalibacter sp905215055	77.4903	197	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543555.1	s__Acutalibacter stercoravium	77.4727	189	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.18	97.66	0.89	0.84	11	-
GCA_019112625.1	s__Acutalibacter stercorigallinarum	77.4542	174	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	96.94	96.88	0.87	0.87	4	-
GCA_900759575.1	s__Acutalibacter sp900759575	77.3885	113	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589395.1	s__Acutalibacter sp910589395	77.3645	186	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904374805.1	s__Acutalibacter sp904374805	77.3593	178	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.85	98.27	0.91	0.86	5	-
GCA_904391645.1	s__Acutalibacter sp904391645	77.1673	120	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587995.1	s__Acutalibacter sp910587995	77.0594	121	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115285.1	s__Acutalibacter pullistercoris	77.0051	144	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549945.1	s__UBA1417 sp900549945	76.9718	66	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.46	97.65	0.85	0.74	4	-
GCF_904420555.1	s__Heritagella intestinalis	76.8807	74	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Heritagella	95.0	98.37	96.53	0.95	0.92	4	-
GCA_017407665.1	s__UBA1417 sp017407665	76.2003	66	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:58,843] [INFO] GTDB search result was written to GCF_900048895.1_PRJEB12697_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:58,844] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:58,848] [INFO] DFAST_QC result json was written to GCF_900048895.1_PRJEB12697_genomic.fna/dqc_result.json
[2024-01-24 12:41:58,848] [INFO] DFAST_QC completed!
[2024-01-24 12:41:58,849] [INFO] Total running time: 0h1m8s