[2023-06-29 12:57:44,114] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:57:44,117] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:57:44,117] [INFO] DQC Reference Directory: /var/lib/cwl/stgf26858fe-3167-4e3c-b1f2-a250bf94359e/dqc_reference
[2023-06-29 12:57:45,445] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:57:45,446] [INFO] Task started: Prodigal
[2023-06-29 12:57:45,446] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe8d17f3-6d05-42a6-a741-f3e2fd88dc56/GCA_023708545.1_ASM2370854v1_genomic.fna.gz | prodigal -d GCA_023708545.1_ASM2370854v1_genomic.fna/cds.fna -a GCA_023708545.1_ASM2370854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:58:12,033] [INFO] Task succeeded: Prodigal
[2023-06-29 12:58:12,034] [INFO] Task started: HMMsearch
[2023-06-29 12:58:12,034] [INFO] Running command: hmmsearch --tblout GCA_023708545.1_ASM2370854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf26858fe-3167-4e3c-b1f2-a250bf94359e/dqc_reference/reference_markers.hmm GCA_023708545.1_ASM2370854v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:58:12,335] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:58:12,338] [INFO] Found 6/6 markers.
[2023-06-29 12:58:12,382] [INFO] Query marker FASTA was written to GCA_023708545.1_ASM2370854v1_genomic.fna/markers.fasta
[2023-06-29 12:58:12,383] [INFO] Task started: Blastn
[2023-06-29 12:58:12,383] [INFO] Running command: blastn -query GCA_023708545.1_ASM2370854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf26858fe-3167-4e3c-b1f2-a250bf94359e/dqc_reference/reference_markers.fasta -out GCA_023708545.1_ASM2370854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:58:13,023] [INFO] Task succeeded: Blastn
[2023-06-29 12:58:13,028] [INFO] Selected 9 target genomes.
[2023-06-29 12:58:13,029] [INFO] Target genome list was writen to GCA_023708545.1_ASM2370854v1_genomic.fna/target_genomes.txt
[2023-06-29 12:58:13,030] [INFO] Task started: fastANI
[2023-06-29 12:58:13,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe8d17f3-6d05-42a6-a741-f3e2fd88dc56/GCA_023708545.1_ASM2370854v1_genomic.fna.gz --refList GCA_023708545.1_ASM2370854v1_genomic.fna/target_genomes.txt --output GCA_023708545.1_ASM2370854v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:58:21,831] [INFO] Task succeeded: fastANI
[2023-06-29 12:58:21,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf26858fe-3167-4e3c-b1f2-a250bf94359e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:58:21,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf26858fe-3167-4e3c-b1f2-a250bf94359e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:58:21,844] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2023-06-29 12:58:21,844] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-29 12:58:21,844] [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 uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	98.4138	1131	1503	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	98.332	1137	1503	95	inconclusive
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	98.3027	1144	1503	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	98.2949	1139	1503	95	inconclusive
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	96.0872	1026	1503	95	inconclusive
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	94.6171	970	1503	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	92.3004	840	1503	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.6556	531	1503	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	80.1295	540	1503	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:58:21,846] [INFO] DFAST Taxonomy check result was written to GCA_023708545.1_ASM2370854v1_genomic.fna/tc_result.tsv
[2023-06-29 12:58:21,847] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:58:21,847] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:58:21,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf26858fe-3167-4e3c-b1f2-a250bf94359e/dqc_reference/checkm_data
[2023-06-29 12:58:21,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:58:21,895] [INFO] Task started: CheckM
[2023-06-29 12:58:21,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708545.1_ASM2370854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708545.1_ASM2370854v1_genomic.fna/checkm_input GCA_023708545.1_ASM2370854v1_genomic.fna/checkm_result
[2023-06-29 12:59:34,388] [INFO] Task succeeded: CheckM
[2023-06-29 12:59:34,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.50%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:59:34,415] [INFO] ===== Completeness check finished =====
[2023-06-29 12:59:34,415] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:59:34,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708545.1_ASM2370854v1_genomic.fna/markers.fasta)
[2023-06-29 12:59:34,416] [INFO] Task started: Blastn
[2023-06-29 12:59:34,416] [INFO] Running command: blastn -query GCA_023708545.1_ASM2370854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf26858fe-3167-4e3c-b1f2-a250bf94359e/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708545.1_ASM2370854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:59:35,256] [INFO] Task succeeded: Blastn
[2023-06-29 12:59:35,261] [INFO] Selected 11 target genomes.
[2023-06-29 12:59:35,261] [INFO] Target genome list was writen to GCA_023708545.1_ASM2370854v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:59:35,265] [INFO] Task started: fastANI
[2023-06-29 12:59:35,265] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe8d17f3-6d05-42a6-a741-f3e2fd88dc56/GCA_023708545.1_ASM2370854v1_genomic.fna.gz --refList GCA_023708545.1_ASM2370854v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708545.1_ASM2370854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:59:44,737] [INFO] Task succeeded: fastANI
[2023-06-29 12:59:44,753] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:59:44,753] [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_000154205.1	s__Bacteroides uniformis	98.3006	1139	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	conclusive
GCF_000614125.1	s__Bacteroides rodentium	94.5964	971	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793475.1	s__Bacteroides sp002491635	91.8785	863	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCA_905197435.1	s__Bacteroides sp905197435	87.8588	652	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195635.1	s__Bacteroides fluxus	82.468	651	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCA_902388495.1	s__Bacteroides sp902388495	81.9044	667	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCA_905203765.1	s__Bacteroides sp905203765	81.2103	494	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003438615.1	s__Bacteroides sp003545565	81.0082	543	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_900129655.1	s__Bacteroides clarus	80.2384	533	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000374365.1	s__Bacteroides gallinarum	79.9603	527	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000186225.1	s__Bacteroides helcogenes	79.9385	521	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:59:44,755] [INFO] GTDB search result was written to GCA_023708545.1_ASM2370854v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:59:44,756] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:59:44,760] [INFO] DFAST_QC result json was written to GCA_023708545.1_ASM2370854v1_genomic.fna/dqc_result.json
[2023-06-29 12:59:44,760] [INFO] DFAST_QC completed!
[2023-06-29 12:59:44,760] [INFO] Total running time: 0h2m1s