[2024-01-24 12:06:50,145] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d5d930b-bdee-459d-863a-6d11775dbb9f/dqc_reference
[2024-01-24 12:06:51,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:51,388] [INFO] Task started: Prodigal
[2024-01-24 12:06:51,388] [INFO] Running command: gunzip -c /var/lib/cwl/stga717bda4-e772-4fe8-bb18-a86998c757aa/GCF_009193325.2_ASM919332v2_genomic.fna.gz | prodigal -d GCF_009193325.2_ASM919332v2_genomic.fna/cds.fna -a GCF_009193325.2_ASM919332v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:17,974] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:17,975] [INFO] Task started: HMMsearch
[2024-01-24 12:07:17,975] [INFO] Running command: hmmsearch --tblout GCF_009193325.2_ASM919332v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d5d930b-bdee-459d-863a-6d11775dbb9f/dqc_reference/reference_markers.hmm GCF_009193325.2_ASM919332v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:18,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:18,287] [INFO] Found 6/6 markers.
[2024-01-24 12:07:18,337] [INFO] Query marker FASTA was written to GCF_009193325.2_ASM919332v2_genomic.fna/markers.fasta
[2024-01-24 12:07:18,338] [INFO] Task started: Blastn
[2024-01-24 12:07:18,338] [INFO] Running command: blastn -query GCF_009193325.2_ASM919332v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d5d930b-bdee-459d-863a-6d11775dbb9f/dqc_reference/reference_markers.fasta -out GCF_009193325.2_ASM919332v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:18,954] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:18,958] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:18,958] [INFO] Target genome list was writen to GCF_009193325.2_ASM919332v2_genomic.fna/target_genomes.txt
[2024-01-24 12:07:18,966] [INFO] Task started: fastANI
[2024-01-24 12:07:18,967] [INFO] Running command: fastANI --query /var/lib/cwl/stga717bda4-e772-4fe8-bb18-a86998c757aa/GCF_009193325.2_ASM919332v2_genomic.fna.gz --refList GCF_009193325.2_ASM919332v2_genomic.fna/target_genomes.txt --output GCF_009193325.2_ASM919332v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:36,526] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:36,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d5d930b-bdee-459d-863a-6d11775dbb9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:36,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d5d930b-bdee-459d-863a-6d11775dbb9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:36,543] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:07:36,543] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:07:36,543] [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 zhangwenhongii	strain=HF-5287	GCA_009193325.2	2650157	2650157	type	True	100.0	1769	1773	95	inconclusive
Bacteroides finegoldii	strain=DSM 17565	GCA_000156195.1	338188	338188	suspected-type	True	95.8372	1092	1773	95	inconclusive
Bacteroides ovatus	strain=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	85.396	980	1773	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	85.3545	975	1773	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	85.337	973	1773	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	85.3286	990	1773	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	85.3152	980	1773	95	below_threshold
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	84.3534	978	1773	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	83.9285	787	1773	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	83.8436	795	1773	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	83.8276	788	1773	95	below_threshold
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	83.827	1023	1773	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	82.4466	759	1773	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	81.5721	764	1773	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	79.1768	274	1773	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	79.0568	278	1773	95	below_threshold
Bacteroides cutis	strain=Marseille-P4118	GCA_900241005.1	2024197	2024197	type	True	78.8629	290	1773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,546] [INFO] DFAST Taxonomy check result was written to GCF_009193325.2_ASM919332v2_genomic.fna/tc_result.tsv
[2024-01-24 12:07:36,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:36,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:36,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d5d930b-bdee-459d-863a-6d11775dbb9f/dqc_reference/checkm_data
[2024-01-24 12:07:36,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:36,605] [INFO] Task started: CheckM
[2024-01-24 12:07:36,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009193325.2_ASM919332v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009193325.2_ASM919332v2_genomic.fna/checkm_input GCF_009193325.2_ASM919332v2_genomic.fna/checkm_result
[2024-01-24 12:08:49,796] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:49,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:49,815] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:49,816] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:49,816] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009193325.2_ASM919332v2_genomic.fna/markers.fasta)
[2024-01-24 12:08:49,816] [INFO] Task started: Blastn
[2024-01-24 12:08:49,816] [INFO] Running command: blastn -query GCF_009193325.2_ASM919332v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d5d930b-bdee-459d-863a-6d11775dbb9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009193325.2_ASM919332v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:50,637] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:50,641] [INFO] Selected 14 target genomes.
[2024-01-24 12:08:50,641] [INFO] Target genome list was writen to GCF_009193325.2_ASM919332v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:50,652] [INFO] Task started: fastANI
[2024-01-24 12:08:50,652] [INFO] Running command: fastANI --query /var/lib/cwl/stga717bda4-e772-4fe8-bb18-a86998c757aa/GCF_009193325.2_ASM919332v2_genomic.fna.gz --refList GCF_009193325.2_ASM919332v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009193325.2_ASM919332v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:06,239] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:06,258] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:06,258] [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_009193325.2	s__Bacteroides zhangwenhongi	100.0	1769	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	conclusive
GCF_000156195.1	s__Bacteroides finegoldii	95.8372	1092	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCA_900556625.1	s__Bacteroides sp900556625	91.8054	615	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.84	99.84	0.94	0.94	2	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	86.3184	1051	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCA_902362375.1	s__Bacteroides sp902362375	85.6611	971	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_001314995.1	s__Bacteroides ovatus	85.3365	976	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_001688725.2	s__Bacteroides caecimuris	83.9011	795	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_900130125.1	s__Bacteroides congonensis	83.8221	1023	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_903181435.1	s__Bacteroides sp900765785	83.8199	872	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_014750685.1	s__Bacteroides sp014750685	83.4458	1018	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012113595.1	s__Bacteroides sp012113595	83.4407	989	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000613385.1	s__Bacteroides acidifaciens	83.3022	765	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.33	97.99	0.81	0.75	18	-
GCA_900761785.1	s__Bacteroides sp900761785	82.8857	901	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578895.1	s__Bacteroides sp910578895	78.5895	244	1773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:06,259] [INFO] GTDB search result was written to GCF_009193325.2_ASM919332v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:06,260] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:06,264] [INFO] DFAST_QC result json was written to GCF_009193325.2_ASM919332v2_genomic.fna/dqc_result.json
[2024-01-24 12:09:06,265] [INFO] DFAST_QC completed!
[2024-01-24 12:09:06,265] [INFO] Total running time: 0h2m16s