[2024-01-25 17:34:07,120] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,123] [INFO] DQC Reference Directory: /var/lib/cwl/stgec1f9d34-d365-4012-ac93-25910ef10b80/dqc_reference
[2024-01-25 17:34:08,952] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,955] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a6decdf-d08a-4b71-a2c6-f0173cb216a8/GCF_014196955.1_ASM1419695v1_genomic.fna.gz | prodigal -d GCF_014196955.1_ASM1419695v1_genomic.fna/cds.fna -a GCF_014196955.1_ASM1419695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:30,079] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:30,079] [INFO] Task started: HMMsearch
[2024-01-25 17:34:30,079] [INFO] Running command: hmmsearch --tblout GCF_014196955.1_ASM1419695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec1f9d34-d365-4012-ac93-25910ef10b80/dqc_reference/reference_markers.hmm GCF_014196955.1_ASM1419695v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:30,424] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:30,425] [INFO] Found 6/6 markers.
[2024-01-25 17:34:30,470] [INFO] Query marker FASTA was written to GCF_014196955.1_ASM1419695v1_genomic.fna/markers.fasta
[2024-01-25 17:34:30,471] [INFO] Task started: Blastn
[2024-01-25 17:34:30,471] [INFO] Running command: blastn -query GCF_014196955.1_ASM1419695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec1f9d34-d365-4012-ac93-25910ef10b80/dqc_reference/reference_markers.fasta -out GCF_014196955.1_ASM1419695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:31,107] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:31,110] [INFO] Selected 18 target genomes.
[2024-01-25 17:34:31,110] [INFO] Target genome list was writen to GCF_014196955.1_ASM1419695v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:31,151] [INFO] Task started: fastANI
[2024-01-25 17:34:31,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6decdf-d08a-4b71-a2c6-f0173cb216a8/GCF_014196955.1_ASM1419695v1_genomic.fna.gz --refList GCF_014196955.1_ASM1419695v1_genomic.fna/target_genomes.txt --output GCF_014196955.1_ASM1419695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:50,210] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:50,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec1f9d34-d365-4012-ac93-25910ef10b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:50,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec1f9d34-d365-4012-ac93-25910ef10b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:50,232] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:50,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:50,233] [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 reticulotermitis	strain=DSM 105720	GCA_014196955.1	1133319	1133319	type	True	100.0	1765	1767	95	conclusive
Bacteroides reticulotermitis	strain=JCM 10512	GCA_000517545.1	1133319	1133319	type	True	99.9575	1721	1767	95	conclusive
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	78.6536	389	1767	95	below_threshold
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	78.6354	455	1767	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	78.5957	382	1767	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	78.5815	391	1767	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	78.4839	446	1767	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	78.4783	479	1767	95	below_threshold
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	78.4461	453	1767	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	78.4363	472	1767	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	78.3962	457	1767	95	below_threshold
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	78.3753	447	1767	95	below_threshold
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	78.229	258	1767	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	77.8482	186	1767	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.7673	215	1767	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	77.6048	168	1767	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	77.6022	178	1767	95	below_threshold
Bacteroides neonati	strain=MS4	GCA_000499785.1	1347393	1347393	type	True	77.5631	216	1767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:50,249] [INFO] DFAST Taxonomy check result was written to GCF_014196955.1_ASM1419695v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:50,254] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:50,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:50,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec1f9d34-d365-4012-ac93-25910ef10b80/dqc_reference/checkm_data
[2024-01-25 17:34:50,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:50,315] [INFO] Task started: CheckM
[2024-01-25 17:34:50,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196955.1_ASM1419695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196955.1_ASM1419695v1_genomic.fna/checkm_input GCF_014196955.1_ASM1419695v1_genomic.fna/checkm_result
[2024-01-25 17:35:48,406] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:48,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:48,432] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:48,432] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:48,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196955.1_ASM1419695v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:48,433] [INFO] Task started: Blastn
[2024-01-25 17:35:48,433] [INFO] Running command: blastn -query GCF_014196955.1_ASM1419695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec1f9d34-d365-4012-ac93-25910ef10b80/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196955.1_ASM1419695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:49,477] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:49,480] [INFO] Selected 19 target genomes.
[2024-01-25 17:35:49,480] [INFO] Target genome list was writen to GCF_014196955.1_ASM1419695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:49,492] [INFO] Task started: fastANI
[2024-01-25 17:35:49,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6decdf-d08a-4b71-a2c6-f0173cb216a8/GCF_014196955.1_ASM1419695v1_genomic.fna.gz --refList GCF_014196955.1_ASM1419695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196955.1_ASM1419695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:06,786] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:06,802] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:06,803] [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_000517545.1	s__Bacteroides reticulotermitis	99.9575	1721	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_900106755.1	s__Bacteroides faecis	78.9534	435	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCF_003865075.1	s__Bacteroides faecalis	78.8671	352	1767	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	78.7016	495	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_001688725.2	s__Bacteroides caecimuris	78.6705	394	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_000210075.1	s__Bacteroides xylanisolvens	78.6323	454	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_000156195.1	s__Bacteroides finegoldii	78.6051	412	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCF_903181435.1	s__Bacteroides sp900765785	78.5234	410	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCA_000613385.1	s__Bacteroides acidifaciens	78.5071	372	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.33	97.99	0.81	0.75	18	-
GCF_014750685.1	s__Bacteroides sp014750685	78.4756	458	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314995.1	s__Bacteroides ovatus	78.4751	478	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCA_910586915.1	s__Bacteroides sp910586915	78.4244	287	1767	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	78.4231	451	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	78.3759	458	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_900130125.1	s__Bacteroides congonensis	78.3694	446	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCA_900547205.1	s__Bacteroides sp900547205	78.3428	353	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.95	0.95	2	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	78.3374	476	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:06,804] [INFO] GTDB search result was written to GCF_014196955.1_ASM1419695v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:06,805] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:06,809] [INFO] DFAST_QC result json was written to GCF_014196955.1_ASM1419695v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:06,809] [INFO] DFAST_QC completed!
[2024-01-25 17:36:06,809] [INFO] Total running time: 0h1m60s