[2024-01-24 14:19:02,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:02,135] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:02,135] [INFO] DQC Reference Directory: /var/lib/cwl/stg50b30e6f-33b6-4b15-be98-5f2d062917cd/dqc_reference
[2024-01-24 14:19:03,356] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:03,357] [INFO] Task started: Prodigal
[2024-01-24 14:19:03,357] [INFO] Running command: gunzip -c /var/lib/cwl/stg4953a365-04a4-4c23-aed8-2f18603e63f9/GCF_000172175.1_ASM17217v1_genomic.fna.gz | prodigal -d GCF_000172175.1_ASM17217v1_genomic.fna/cds.fna -a GCF_000172175.1_ASM17217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:33,449] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:33,450] [INFO] Task started: HMMsearch
[2024-01-24 14:19:33,450] [INFO] Running command: hmmsearch --tblout GCF_000172175.1_ASM17217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50b30e6f-33b6-4b15-be98-5f2d062917cd/dqc_reference/reference_markers.hmm GCF_000172175.1_ASM17217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:33,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:33,813] [INFO] Found 6/6 markers.
[2024-01-24 14:19:33,861] [INFO] Query marker FASTA was written to GCF_000172175.1_ASM17217v1_genomic.fna/markers.fasta
[2024-01-24 14:19:33,862] [INFO] Task started: Blastn
[2024-01-24 14:19:33,862] [INFO] Running command: blastn -query GCF_000172175.1_ASM17217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b30e6f-33b6-4b15-be98-5f2d062917cd/dqc_reference/reference_markers.fasta -out GCF_000172175.1_ASM17217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:34,639] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:34,643] [INFO] Selected 16 target genomes.
[2024-01-24 14:19:34,644] [INFO] Target genome list was writen to GCF_000172175.1_ASM17217v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:34,654] [INFO] Task started: fastANI
[2024-01-24 14:19:34,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg4953a365-04a4-4c23-aed8-2f18603e63f9/GCF_000172175.1_ASM17217v1_genomic.fna.gz --refList GCF_000172175.1_ASM17217v1_genomic.fna/target_genomes.txt --output GCF_000172175.1_ASM17217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:52,434] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:52,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50b30e6f-33b6-4b15-be98-5f2d062917cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:52,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50b30e6f-33b6-4b15-be98-5f2d062917cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:52,446] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:52,446] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:52,446] [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 intestinalis	strain=DSM 17393	GCA_000172175.1	329854	329854	type	True	100.0	2010	2012	95	conclusive
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	88.8872	1234	2012	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	88.5852	1312	2012	95	below_threshold
Bacteroides stercorirosoris	strain=DSM 26884	GCA_900142015.1	871324	871324	type	True	85.6007	1178	2012	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	85.5154	1153	2012	95	below_threshold
Bacteroides oleiciplenus	strain=YIT 12058	GCA_000315485.1	626931	626931	type	True	84.7512	1389	2012	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.2659	451	2012	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	80.2061	446	2012	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	80.1791	455	2012	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	80.0161	528	2012	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	79.4868	474	2012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:52,448] [INFO] DFAST Taxonomy check result was written to GCF_000172175.1_ASM17217v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:52,451] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:52,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:52,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50b30e6f-33b6-4b15-be98-5f2d062917cd/dqc_reference/checkm_data
[2024-01-24 14:19:52,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:52,521] [INFO] Task started: CheckM
[2024-01-24 14:19:52,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000172175.1_ASM17217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000172175.1_ASM17217v1_genomic.fna/checkm_input GCF_000172175.1_ASM17217v1_genomic.fna/checkm_result
[2024-01-24 14:21:14,597] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:14,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:14,618] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:14,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:14,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000172175.1_ASM17217v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:14,619] [INFO] Task started: Blastn
[2024-01-24 14:21:14,620] [INFO] Running command: blastn -query GCF_000172175.1_ASM17217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b30e6f-33b6-4b15-be98-5f2d062917cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000172175.1_ASM17217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:15,482] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:15,508] [INFO] Selected 9 target genomes.
[2024-01-24 14:21:15,508] [INFO] Target genome list was writen to GCF_000172175.1_ASM17217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:15,531] [INFO] Task started: fastANI
[2024-01-24 14:21:15,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg4953a365-04a4-4c23-aed8-2f18603e63f9/GCF_000172175.1_ASM17217v1_genomic.fna.gz --refList GCF_000172175.1_ASM17217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000172175.1_ASM17217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:28,266] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:28,275] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:21:28,275] [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_000172175.1	s__Bacteroides intestinalis	100.0	2010	2012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.18	96.30	0.86	0.76	22	inconclusive
GCA_900557355.1	s__Bacteroides sp900557355	95.5049	845	2012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.57	98.57	0.54	0.54	2	inconclusive
GCF_003464595.1	s__Bacteroides intestinalis_A	94.1846	1494	2012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	97.86	96.66	0.85	0.74	7	-
GCF_902364365.1	s__Bacteroides sp900556215	93.317	1468	2012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCF_019129285.1	s__Bacteroides sp900552405	89.2178	1312	2012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.09	95.34	0.92	0.76	12	-
GCF_000513195.1	s__Bacteroides timonensis	88.8918	1233	2012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158035.1	s__Bacteroides cellulosilyticus	88.5318	1317	2012	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.21	95.02	0.83	0.72	42	-
GCA_905207245.1	s__Bacteroides sp905207245	85.7534	1198	2012	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	78.7014	367	2012	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 14:21:28,277] [INFO] GTDB search result was written to GCF_000172175.1_ASM17217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:28,278] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:28,281] [INFO] DFAST_QC result json was written to GCF_000172175.1_ASM17217v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:28,281] [INFO] DFAST_QC completed!
[2024-01-24 14:21:28,281] [INFO] Total running time: 0h2m26s