[2024-01-24 13:40:46,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,349] [INFO] DQC Reference Directory: /var/lib/cwl/stgbda83715-c922-4bdb-b678-0898347e6079/dqc_reference
[2024-01-24 13:40:47,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,613] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,613] [INFO] Running command: gunzip -c /var/lib/cwl/stgc50d2b6e-375a-476c-bd90-63963a6e75fd/GCF_014288055.1_ASM1428805v1_genomic.fna.gz | prodigal -d GCF_014288055.1_ASM1428805v1_genomic.fna/cds.fna -a GCF_014288055.1_ASM1428805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:54,634] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:54,634] [INFO] Task started: HMMsearch
[2024-01-24 13:40:54,634] [INFO] Running command: hmmsearch --tblout GCF_014288055.1_ASM1428805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbda83715-c922-4bdb-b678-0898347e6079/dqc_reference/reference_markers.hmm GCF_014288055.1_ASM1428805v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:54,877] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:54,879] [INFO] Found 6/6 markers.
[2024-01-24 13:40:54,902] [INFO] Query marker FASTA was written to GCF_014288055.1_ASM1428805v1_genomic.fna/markers.fasta
[2024-01-24 13:40:54,902] [INFO] Task started: Blastn
[2024-01-24 13:40:54,902] [INFO] Running command: blastn -query GCF_014288055.1_ASM1428805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbda83715-c922-4bdb-b678-0898347e6079/dqc_reference/reference_markers.fasta -out GCF_014288055.1_ASM1428805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:55,546] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:55,551] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:55,551] [INFO] Target genome list was writen to GCF_014288055.1_ASM1428805v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:55,695] [INFO] Task started: fastANI
[2024-01-24 13:40:55,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgc50d2b6e-375a-476c-bd90-63963a6e75fd/GCF_014288055.1_ASM1428805v1_genomic.fna.gz --refList GCF_014288055.1_ASM1428805v1_genomic.fna/target_genomes.txt --output GCF_014288055.1_ASM1428805v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:04,791] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:04,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbda83715-c922-4bdb-b678-0898347e6079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:04,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbda83715-c922-4bdb-b678-0898347e6079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:04,799] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:04,799] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:04,799] [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
Butyricicoccus faecihominis	strain=JCM 31056	GCA_016586375.1	1712515	1712515	type	True	83.2903	475	845	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_014648015.1	1712515	1712515	type	True	83.224	468	845	95	below_threshold
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	79.5066	287	845	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	79.1396	208	845	95	below_threshold
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	78.8918	208	845	95	below_threshold
Butyricicoccus intestinisimiae	strain=MSJd-7	GCA_018918345.1	2841509	2841509	type	True	78.1248	121	845	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.8087	77	845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:04,801] [INFO] DFAST Taxonomy check result was written to GCF_014288055.1_ASM1428805v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:04,801] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:04,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:04,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbda83715-c922-4bdb-b678-0898347e6079/dqc_reference/checkm_data
[2024-01-24 13:41:04,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:04,833] [INFO] Task started: CheckM
[2024-01-24 13:41:04,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014288055.1_ASM1428805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014288055.1_ASM1428805v1_genomic.fna/checkm_input GCF_014288055.1_ASM1428805v1_genomic.fna/checkm_result
[2024-01-24 13:41:30,817] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:30,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:30,841] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:30,841] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:30,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014288055.1_ASM1428805v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:30,842] [INFO] Task started: Blastn
[2024-01-24 13:41:30,842] [INFO] Running command: blastn -query GCF_014288055.1_ASM1428805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbda83715-c922-4bdb-b678-0898347e6079/dqc_reference/reference_markers_gtdb.fasta -out GCF_014288055.1_ASM1428805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:31,834] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:31,837] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:31,837] [INFO] Target genome list was writen to GCF_014288055.1_ASM1428805v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:32,005] [INFO] Task started: fastANI
[2024-01-24 13:41:32,005] [INFO] Running command: fastANI --query /var/lib/cwl/stgc50d2b6e-375a-476c-bd90-63963a6e75fd/GCF_014288055.1_ASM1428805v1_genomic.fna.gz --refList GCF_014288055.1_ASM1428805v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014288055.1_ASM1428805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:40,021] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:40,035] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:40,035] [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_003481705.1	s__Agathobaculum sp003481705	96.2354	698	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.33	96.26	0.92	0.82	8	conclusive
GCA_900544475.1	s__Agathobaculum sp900544475	88.4027	465	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.90	97.82	0.89	0.86	3	-
GCA_003096535.1	s__Agathobaculum butyriciproducens	83.6658	491	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	96.66	95.68	0.85	0.79	34	-
GCA_900555465.1	s__Agathobaculum intestinigallinarum	82.0087	237	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.06	97.06	0.83	0.83	2	-
GCF_900625105.1	s__Agathobaculum sp900625105	81.4747	387	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113065.1	s__Agathobaculum stercoravium	81.0757	314	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.25	98.25	0.89	0.89	2	-
GCA_019115615.1	s__Agathobaculum merdavium	80.5707	303	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114345.1	s__Agathobaculum pullistercoris	80.4312	292	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.72	98.13	0.86	0.78	4	-
GCA_019115425.1	s__Agathobaculum merdigallinarum	80.403	279	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557315.1	s__Agathobaculum sp900557315	80.1242	227	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000701665.1	s__Agathobaculum desmolans	79.5416	285	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.85	98.85	0.90	0.90	2	-
GCF_016901955.1	s__Flavonifractor phocaeensis_A	77.2451	59	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:40,037] [INFO] GTDB search result was written to GCF_014288055.1_ASM1428805v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:40,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:40,043] [INFO] DFAST_QC result json was written to GCF_014288055.1_ASM1428805v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:40,043] [INFO] DFAST_QC completed!
[2024-01-24 13:41:40,044] [INFO] Total running time: 0h0m54s