[2023-06-13 15:45:08,139] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:45:08,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:45:08,153] [INFO] DQC Reference Directory: /var/lib/cwl/stgecd67c07-4e6e-49a9-8c31-61d507cda507/dqc_reference
[2023-06-13 15:45:09,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:45:09,424] [INFO] Task started: Prodigal
[2023-06-13 15:45:09,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ce86f94-7b2e-4770-9b4b-b998b8841cde/GCA_022746085.1_ASM2274608v1_genomic.fna.gz | prodigal -d GCA_022746085.1_ASM2274608v1_genomic.fna/cds.fna -a GCA_022746085.1_ASM2274608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:45:29,984] [INFO] Task succeeded: Prodigal
[2023-06-13 15:45:29,985] [INFO] Task started: HMMsearch
[2023-06-13 15:45:29,985] [INFO] Running command: hmmsearch --tblout GCA_022746085.1_ASM2274608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecd67c07-4e6e-49a9-8c31-61d507cda507/dqc_reference/reference_markers.hmm GCA_022746085.1_ASM2274608v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:45:30,277] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:45:30,278] [INFO] Found 6/6 markers.
[2023-06-13 15:45:30,320] [INFO] Query marker FASTA was written to GCA_022746085.1_ASM2274608v1_genomic.fna/markers.fasta
[2023-06-13 15:45:30,321] [INFO] Task started: Blastn
[2023-06-13 15:45:30,321] [INFO] Running command: blastn -query GCA_022746085.1_ASM2274608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecd67c07-4e6e-49a9-8c31-61d507cda507/dqc_reference/reference_markers.fasta -out GCA_022746085.1_ASM2274608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:30,931] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:30,937] [INFO] Selected 11 target genomes.
[2023-06-13 15:45:30,938] [INFO] Target genome list was writen to GCA_022746085.1_ASM2274608v1_genomic.fna/target_genomes.txt
[2023-06-13 15:45:30,939] [INFO] Task started: fastANI
[2023-06-13 15:45:30,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce86f94-7b2e-4770-9b4b-b998b8841cde/GCA_022746085.1_ASM2274608v1_genomic.fna.gz --refList GCA_022746085.1_ASM2274608v1_genomic.fna/target_genomes.txt --output GCA_022746085.1_ASM2274608v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:40,134] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:40,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecd67c07-4e6e-49a9-8c31-61d507cda507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:40,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecd67c07-4e6e-49a9-8c31-61d507cda507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:40,143] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2023-06-13 15:45:40,143] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-13 15:45:40,144] [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	98.5254	915	980	95	inconclusive
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	98.5061	916	980	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	98.4483	916	980	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	98.4289	913	980	95	inconclusive
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	95.9645	837	980	95	inconclusive
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	94.6354	784	980	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	92.1411	700	980	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.0372	413	980	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	79.8604	425	980	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.1272	411	980	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:45:40,146] [INFO] DFAST Taxonomy check result was written to GCA_022746085.1_ASM2274608v1_genomic.fna/tc_result.tsv
[2023-06-13 15:45:40,146] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:40,146] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:40,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecd67c07-4e6e-49a9-8c31-61d507cda507/dqc_reference/checkm_data
[2023-06-13 15:45:40,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:40,190] [INFO] Task started: CheckM
[2023-06-13 15:45:40,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022746085.1_ASM2274608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022746085.1_ASM2274608v1_genomic.fna/checkm_input GCA_022746085.1_ASM2274608v1_genomic.fna/checkm_result
[2023-06-13 15:46:38,120] [INFO] Task succeeded: CheckM
[2023-06-13 15:46:38,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:46:38,146] [INFO] ===== Completeness check finished =====
[2023-06-13 15:46:38,146] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:46:38,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022746085.1_ASM2274608v1_genomic.fna/markers.fasta)
[2023-06-13 15:46:38,147] [INFO] Task started: Blastn
[2023-06-13 15:46:38,147] [INFO] Running command: blastn -query GCA_022746085.1_ASM2274608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecd67c07-4e6e-49a9-8c31-61d507cda507/dqc_reference/reference_markers_gtdb.fasta -out GCA_022746085.1_ASM2274608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:46:39,019] [INFO] Task succeeded: Blastn
[2023-06-13 15:46:39,024] [INFO] Selected 13 target genomes.
[2023-06-13 15:46:39,024] [INFO] Target genome list was writen to GCA_022746085.1_ASM2274608v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:46:39,026] [INFO] Task started: fastANI
[2023-06-13 15:46:39,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce86f94-7b2e-4770-9b4b-b998b8841cde/GCA_022746085.1_ASM2274608v1_genomic.fna.gz --refList GCA_022746085.1_ASM2274608v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022746085.1_ASM2274608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:46:48,406] [INFO] Task succeeded: fastANI
[2023-06-13 15:46:48,423] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:46:48,424] [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	98.4483	916	980	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	94.6354	784	980	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	92.0402	720	980	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	87.7153	531	980	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	81.3877	503	980	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	81.2916	539	980	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	80.885	424	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129655.1	s__Bacteroides clarus	79.9839	417	980	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	79.6187	409	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003438615.1	s__Bacteroides sp003545565	79.5085	424	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000186225.1	s__Bacteroides helcogenes	79.3592	419	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905198575.1	s__Phocaeicola sp905198575	77.3158	50	980	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:46:48,425] [INFO] GTDB search result was written to GCA_022746085.1_ASM2274608v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:46:48,426] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:46:48,430] [INFO] DFAST_QC result json was written to GCA_022746085.1_ASM2274608v1_genomic.fna/dqc_result.json
[2023-06-13 15:46:48,431] [INFO] DFAST_QC completed!
[2023-06-13 15:46:48,431] [INFO] Total running time: 0h1m40s