[2024-01-24 13:49:18,343] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:18,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:18,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg15a4e2cf-d1a6-4165-800e-e45995bd6653/dqc_reference
[2024-01-24 13:49:19,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:19,756] [INFO] Task started: Prodigal
[2024-01-24 13:49:19,756] [INFO] Running command: gunzip -c /var/lib/cwl/stgeff76273-d2dd-41e6-a4fe-799a50903e23/GCF_025567045.1_ASM2556704v1_genomic.fna.gz | prodigal -d GCF_025567045.1_ASM2556704v1_genomic.fna/cds.fna -a GCF_025567045.1_ASM2556704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:34,188] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:34,189] [INFO] Task started: HMMsearch
[2024-01-24 13:49:34,189] [INFO] Running command: hmmsearch --tblout GCF_025567045.1_ASM2556704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15a4e2cf-d1a6-4165-800e-e45995bd6653/dqc_reference/reference_markers.hmm GCF_025567045.1_ASM2556704v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:34,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:34,557] [INFO] Found 6/6 markers.
[2024-01-24 13:49:34,594] [INFO] Query marker FASTA was written to GCF_025567045.1_ASM2556704v1_genomic.fna/markers.fasta
[2024-01-24 13:49:34,595] [INFO] Task started: Blastn
[2024-01-24 13:49:34,595] [INFO] Running command: blastn -query GCF_025567045.1_ASM2556704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15a4e2cf-d1a6-4165-800e-e45995bd6653/dqc_reference/reference_markers.fasta -out GCF_025567045.1_ASM2556704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:35,211] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:35,215] [INFO] Selected 22 target genomes.
[2024-01-24 13:49:35,215] [INFO] Target genome list was writen to GCF_025567045.1_ASM2556704v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:35,223] [INFO] Task started: fastANI
[2024-01-24 13:49:35,223] [INFO] Running command: fastANI --query /var/lib/cwl/stgeff76273-d2dd-41e6-a4fe-799a50903e23/GCF_025567045.1_ASM2556704v1_genomic.fna.gz --refList GCF_025567045.1_ASM2556704v1_genomic.fna/target_genomes.txt --output GCF_025567045.1_ASM2556704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:50,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:50,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15a4e2cf-d1a6-4165-800e-e45995bd6653/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:50,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15a4e2cf-d1a6-4165-800e-e45995bd6653/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:50,801] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:50,801] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:50,801] [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
Bacteroides faecalis	strain=KCTC 15687	GCA_003865075.1	2447885	2447885	type	True	80.7338	76	1105	95	below_threshold
Bacteroides salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	80.4249	72	1105	95	below_threshold
Coprobacter secundus subsp. similis	strain=2CBH44	GCA_015097275.1	2751153	1501392	type	True	77.8938	100	1105	95	below_threshold
Barnesiella intestinihominis	strain=YIT 11860	GCA_000296465.1	487174	487174	type	True	77.8821	98	1105	95	below_threshold
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	77.603	62	1105	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	77.5369	64	1105	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	77.3541	62	1105	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:50,803] [INFO] DFAST Taxonomy check result was written to GCF_025567045.1_ASM2556704v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:50,803] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:50,803] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:50,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15a4e2cf-d1a6-4165-800e-e45995bd6653/dqc_reference/checkm_data
[2024-01-24 13:49:50,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:50,841] [INFO] Task started: CheckM
[2024-01-24 13:49:50,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567045.1_ASM2556704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567045.1_ASM2556704v1_genomic.fna/checkm_input GCF_025567045.1_ASM2556704v1_genomic.fna/checkm_result
[2024-01-24 13:50:35,874] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:35,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:35,893] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:35,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:35,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567045.1_ASM2556704v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:35,894] [INFO] Task started: Blastn
[2024-01-24 13:50:35,894] [INFO] Running command: blastn -query GCF_025567045.1_ASM2556704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15a4e2cf-d1a6-4165-800e-e45995bd6653/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567045.1_ASM2556704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:36,857] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:36,861] [INFO] Selected 26 target genomes.
[2024-01-24 13:50:36,862] [INFO] Target genome list was writen to GCF_025567045.1_ASM2556704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:36,881] [INFO] Task started: fastANI
[2024-01-24 13:50:36,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgeff76273-d2dd-41e6-a4fe-799a50903e23/GCF_025567045.1_ASM2556704v1_genomic.fna.gz --refList GCF_025567045.1_ASM2556704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567045.1_ASM2556704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:51,140] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:51,148] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:51,149] [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_902363425.1	s__CABJAA01 sp003150885	100.0	1105	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__CABJAA01	95.0	99.11	99.10	0.93	0.92	5	conclusive
GCA_902362595.1	s__Phocaeicola merdigallinarum	85.2821	67	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_003865075.1	s__Bacteroides faecalis	80.7671	76	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000803105.1	s__Coprobacter secundus	78.4245	100	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.96	96.86	0.90	0.85	6	-
GCA_900538555.1	s__UMGS27 sp900538555	78.0889	90	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__UMGS27	95.0	99.31	98.62	0.96	0.93	3	-
GCF_000296465.1	s__Barnesiella intestinihominis	77.8633	98	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	98.49	98.18	0.93	0.86	27	-
GCA_000613465.1	s__Bacteroides nordii	77.6917	50	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.55	98.11	0.85	0.80	13	-
GCA_900545915.1	s__Coprobacter sp900545915	76.9951	83	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.49	96.20	0.84	0.83	3	-
GCA_019115485.1	s__Barnesiella excrementavium	76.9486	61	1105	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,150] [INFO] GTDB search result was written to GCF_025567045.1_ASM2556704v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:51,150] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:51,153] [INFO] DFAST_QC result json was written to GCF_025567045.1_ASM2556704v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:51,153] [INFO] DFAST_QC completed!
[2024-01-24 13:50:51,153] [INFO] Total running time: 0h1m33s