[2023-06-14 01:07:09,593] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:07:09,595] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:07:09,596] [INFO] DQC Reference Directory: /var/lib/cwl/stga658aede-b717-4751-8189-f860f15e0ca1/dqc_reference
[2023-06-14 01:07:10,904] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:07:10,905] [INFO] Task started: Prodigal
[2023-06-14 01:07:10,905] [INFO] Running command: gunzip -c /var/lib/cwl/stg4116baa0-d67b-4394-b9e0-22833564b227/GCA_022797575.1_ASM2279757v1_genomic.fna.gz | prodigal -d GCA_022797575.1_ASM2279757v1_genomic.fna/cds.fna -a GCA_022797575.1_ASM2279757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:36,248] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:36,248] [INFO] Task started: HMMsearch
[2023-06-14 01:07:36,249] [INFO] Running command: hmmsearch --tblout GCA_022797575.1_ASM2279757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga658aede-b717-4751-8189-f860f15e0ca1/dqc_reference/reference_markers.hmm GCA_022797575.1_ASM2279757v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:36,521] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:36,522] [INFO] Found 6/6 markers.
[2023-06-14 01:07:36,567] [INFO] Query marker FASTA was written to GCA_022797575.1_ASM2279757v1_genomic.fna/markers.fasta
[2023-06-14 01:07:36,567] [INFO] Task started: Blastn
[2023-06-14 01:07:36,567] [INFO] Running command: blastn -query GCA_022797575.1_ASM2279757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga658aede-b717-4751-8189-f860f15e0ca1/dqc_reference/reference_markers.fasta -out GCA_022797575.1_ASM2279757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:37,182] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:37,186] [INFO] Selected 11 target genomes.
[2023-06-14 01:07:37,186] [INFO] Target genome list was writen to GCA_022797575.1_ASM2279757v1_genomic.fna/target_genomes.txt
[2023-06-14 01:07:37,187] [INFO] Task started: fastANI
[2023-06-14 01:07:37,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg4116baa0-d67b-4394-b9e0-22833564b227/GCA_022797575.1_ASM2279757v1_genomic.fna.gz --refList GCA_022797575.1_ASM2279757v1_genomic.fna/target_genomes.txt --output GCA_022797575.1_ASM2279757v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:07:50,027] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:50,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga658aede-b717-4751-8189-f860f15e0ca1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:07:50,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga658aede-b717-4751-8189-f860f15e0ca1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:07:50,038] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2023-06-14 01:07:50,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-14 01:07:50,038] [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 thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	98.2166	1568	1792	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_000011065.1	818	818	type	True	98.1941	1584	1792	95	conclusive
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	98.1856	1570	1792	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	98.1678	1585	1792	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	98.1574	1594	1792	95	conclusive
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	82.2097	700	1792	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	81.9437	746	1792	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	81.6555	880	1792	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	81.5926	883	1792	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.0335	395	1792	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	78.195	280	1792	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:07:50,041] [INFO] DFAST Taxonomy check result was written to GCA_022797575.1_ASM2279757v1_genomic.fna/tc_result.tsv
[2023-06-14 01:07:50,041] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:07:50,041] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:07:50,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga658aede-b717-4751-8189-f860f15e0ca1/dqc_reference/checkm_data
[2023-06-14 01:07:50,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:07:50,093] [INFO] Task started: CheckM
[2023-06-14 01:07:50,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022797575.1_ASM2279757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022797575.1_ASM2279757v1_genomic.fna/checkm_input GCA_022797575.1_ASM2279757v1_genomic.fna/checkm_result
[2023-06-14 01:09:01,100] [INFO] Task succeeded: CheckM
[2023-06-14 01:09:01,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:09:01,123] [INFO] ===== Completeness check finished =====
[2023-06-14 01:09:01,123] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:09:01,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022797575.1_ASM2279757v1_genomic.fna/markers.fasta)
[2023-06-14 01:09:01,124] [INFO] Task started: Blastn
[2023-06-14 01:09:01,124] [INFO] Running command: blastn -query GCA_022797575.1_ASM2279757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga658aede-b717-4751-8189-f860f15e0ca1/dqc_reference/reference_markers_gtdb.fasta -out GCA_022797575.1_ASM2279757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:09:01,965] [INFO] Task succeeded: Blastn
[2023-06-14 01:09:01,969] [INFO] Selected 17 target genomes.
[2023-06-14 01:09:01,969] [INFO] Target genome list was writen to GCA_022797575.1_ASM2279757v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:09:01,970] [INFO] Task started: fastANI
[2023-06-14 01:09:01,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg4116baa0-d67b-4394-b9e0-22833564b227/GCA_022797575.1_ASM2279757v1_genomic.fna.gz --refList GCA_022797575.1_ASM2279757v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022797575.1_ASM2279757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:09:19,813] [INFO] Task succeeded: fastANI
[2023-06-14 01:09:19,827] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:09:19,828] [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_000011065.1	s__Bacteroides thetaiotaomicron	98.1941	1584	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	conclusive
GCF_900106755.1	s__Bacteroides faecis	89.2355	1335	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCA_900755095.1	s__Bacteroides sp900755095	89.1658	668	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761785.1	s__Bacteroides sp900761785	83.5835	902	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362375.1	s__Bacteroides sp902362375	81.9941	921	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_903181435.1	s__Bacteroides sp900765785	81.9784	768	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_002222615.2	s__Bacteroides caccae	81.9335	746	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCF_000210075.1	s__Bacteroides xylanisolvens	81.8945	858	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_009193295.2	s__Bacteroides luhongzhouii	81.8067	843	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_000156195.1	s__Bacteroides finegoldii	81.6888	696	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCF_012113595.1	s__Bacteroides sp012113595	81.6817	886	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	81.6447	884	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_001314995.1	s__Bacteroides ovatus	81.594	883	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_900130125.1	s__Bacteroides congonensis	81.5934	875	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	81.5718	737	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCF_014750685.1	s__Bacteroides sp014750685	81.4553	923	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556625.1	s__Bacteroides sp900556625	81.3258	461	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.84	99.84	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-14 01:09:19,830] [INFO] GTDB search result was written to GCA_022797575.1_ASM2279757v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:09:19,830] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:09:19,834] [INFO] DFAST_QC result json was written to GCA_022797575.1_ASM2279757v1_genomic.fna/dqc_result.json
[2023-06-14 01:09:19,834] [INFO] DFAST_QC completed!
[2023-06-14 01:09:19,834] [INFO] Total running time: 0h2m10s