[2023-06-28 02:22:14,004] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:22:14,006] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:22:14,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgee72d92f-1d73-4ec2-aafa-bc3f2228cb01/dqc_reference
[2023-06-28 02:22:15,257] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:22:15,258] [INFO] Task started: Prodigal
[2023-06-28 02:22:15,258] [INFO] Running command: gunzip -c /var/lib/cwl/stg720e0b51-2e9e-4cdd-9f56-24fb327ca2e7/GCA_017392005.1_ASM1739200v1_genomic.fna.gz | prodigal -d GCA_017392005.1_ASM1739200v1_genomic.fna/cds.fna -a GCA_017392005.1_ASM1739200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:22:22,891] [INFO] Task succeeded: Prodigal
[2023-06-28 02:22:22,891] [INFO] Task started: HMMsearch
[2023-06-28 02:22:22,891] [INFO] Running command: hmmsearch --tblout GCA_017392005.1_ASM1739200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee72d92f-1d73-4ec2-aafa-bc3f2228cb01/dqc_reference/reference_markers.hmm GCA_017392005.1_ASM1739200v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:22:23,057] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:22:23,058] [INFO] Found 6/6 markers.
[2023-06-28 02:22:23,074] [INFO] Query marker FASTA was written to GCA_017392005.1_ASM1739200v1_genomic.fna/markers.fasta
[2023-06-28 02:22:23,075] [INFO] Task started: Blastn
[2023-06-28 02:22:23,075] [INFO] Running command: blastn -query GCA_017392005.1_ASM1739200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee72d92f-1d73-4ec2-aafa-bc3f2228cb01/dqc_reference/reference_markers.fasta -out GCA_017392005.1_ASM1739200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:22:23,649] [INFO] Task succeeded: Blastn
[2023-06-28 02:22:23,653] [INFO] Selected 21 target genomes.
[2023-06-28 02:22:23,653] [INFO] Target genome list was writen to GCA_017392005.1_ASM1739200v1_genomic.fna/target_genomes.txt
[2023-06-28 02:22:23,654] [INFO] Task started: fastANI
[2023-06-28 02:22:23,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg720e0b51-2e9e-4cdd-9f56-24fb327ca2e7/GCA_017392005.1_ASM1739200v1_genomic.fna.gz --refList GCA_017392005.1_ASM1739200v1_genomic.fna/target_genomes.txt --output GCA_017392005.1_ASM1739200v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:22:35,293] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:35,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee72d92f-1d73-4ec2-aafa-bc3f2228cb01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:22:35,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee72d92f-1d73-4ec2-aafa-bc3f2228cb01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:22:35,299] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:22:35,299] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 02:22:35,300] [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
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	77.4592	53	221	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	77.4015	51	221	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	77.2864	55	221	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	77.2047	51	221	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 02:22:35,302] [INFO] DFAST Taxonomy check result was written to GCA_017392005.1_ASM1739200v1_genomic.fna/tc_result.tsv
[2023-06-28 02:22:35,303] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:22:35,303] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:22:35,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee72d92f-1d73-4ec2-aafa-bc3f2228cb01/dqc_reference/checkm_data
[2023-06-28 02:22:35,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:22:35,324] [INFO] Task started: CheckM
[2023-06-28 02:22:35,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017392005.1_ASM1739200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017392005.1_ASM1739200v1_genomic.fna/checkm_input GCA_017392005.1_ASM1739200v1_genomic.fna/checkm_result
[2023-06-28 02:23:02,147] [INFO] Task succeeded: CheckM
[2023-06-28 02:23:02,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 02:23:02,165] [INFO] ===== Completeness check finished =====
[2023-06-28 02:23:02,165] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:23:02,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017392005.1_ASM1739200v1_genomic.fna/markers.fasta)
[2023-06-28 02:23:02,166] [INFO] Task started: Blastn
[2023-06-28 02:23:02,166] [INFO] Running command: blastn -query GCA_017392005.1_ASM1739200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee72d92f-1d73-4ec2-aafa-bc3f2228cb01/dqc_reference/reference_markers_gtdb.fasta -out GCA_017392005.1_ASM1739200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:23:03,010] [INFO] Task succeeded: Blastn
[2023-06-28 02:23:03,013] [INFO] Selected 12 target genomes.
[2023-06-28 02:23:03,013] [INFO] Target genome list was writen to GCA_017392005.1_ASM1739200v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:23:03,018] [INFO] Task started: fastANI
[2023-06-28 02:23:03,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg720e0b51-2e9e-4cdd-9f56-24fb327ca2e7/GCA_017392005.1_ASM1739200v1_genomic.fna.gz --refList GCA_017392005.1_ASM1739200v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017392005.1_ASM1739200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:23:06,554] [INFO] Task succeeded: fastANI
[2023-06-28 02:23:06,561] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 02:23:06,562] [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_900770585.1	s__Alistipes sp900770585	95.7157	149	221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.00	96.66	0.89	0.84	3	conclusive
GCA_900769405.1	s__Alistipes sp900769405	89.5785	188	221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.81	97.81	0.91	0.91	2	-
GCA_017442365.1	s__Alistipes sp017442365	89.1645	191	221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.53	97.42	0.94	0.90	8	-
GCA_017463585.1	s__Alistipes sp017463585	88.9575	197	221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	96.67	96.64	0.94	0.91	5	-
GCA_017379895.1	s__Alistipes sp017379895	86.9559	176	221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017425655.1	s__Alistipes sp017425655	86.0175	179	221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550925.1	s__Alistipes sp900550925	77.7939	60	221	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.94	99.88	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2023-06-28 02:23:06,563] [INFO] GTDB search result was written to GCA_017392005.1_ASM1739200v1_genomic.fna/result_gtdb.tsv
[2023-06-28 02:23:06,564] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:23:06,566] [INFO] DFAST_QC result json was written to GCA_017392005.1_ASM1739200v1_genomic.fna/dqc_result.json
[2023-06-28 02:23:06,566] [INFO] DFAST_QC completed!
[2023-06-28 02:23:06,566] [INFO] Total running time: 0h0m53s