[2023-06-30 10:58:31,037] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:58:31,039] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:58:31,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg11657dd5-b5b1-4c14-a5f3-09c518198a1d/dqc_reference
[2023-06-30 10:58:32,258] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:58:32,259] [INFO] Task started: Prodigal
[2023-06-30 10:58:32,259] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbaa4c81-1385-482c-8f11-90dd322df1b6/GCA_900764875.1_SRS259467_2_genomic.fna.gz | prodigal -d GCA_900764875.1_SRS259467_2_genomic.fna/cds.fna -a GCA_900764875.1_SRS259467_2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:58:46,361] [INFO] Task succeeded: Prodigal
[2023-06-30 10:58:46,362] [INFO] Task started: HMMsearch
[2023-06-30 10:58:46,362] [INFO] Running command: hmmsearch --tblout GCA_900764875.1_SRS259467_2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11657dd5-b5b1-4c14-a5f3-09c518198a1d/dqc_reference/reference_markers.hmm GCA_900764875.1_SRS259467_2_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:58:46,606] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:58:46,607] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdbaa4c81-1385-482c-8f11-90dd322df1b6/GCA_900764875.1_SRS259467_2_genomic.fna.gz]
[2023-06-30 10:58:46,633] [INFO] Query marker FASTA was written to GCA_900764875.1_SRS259467_2_genomic.fna/markers.fasta
[2023-06-30 10:58:46,633] [INFO] Task started: Blastn
[2023-06-30 10:58:46,633] [INFO] Running command: blastn -query GCA_900764875.1_SRS259467_2_genomic.fna/markers.fasta -db /var/lib/cwl/stg11657dd5-b5b1-4c14-a5f3-09c518198a1d/dqc_reference/reference_markers.fasta -out GCA_900764875.1_SRS259467_2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:58:47,244] [INFO] Task succeeded: Blastn
[2023-06-30 10:58:47,248] [INFO] Selected 14 target genomes.
[2023-06-30 10:58:47,248] [INFO] Target genome list was writen to GCA_900764875.1_SRS259467_2_genomic.fna/target_genomes.txt
[2023-06-30 10:58:47,250] [INFO] Task started: fastANI
[2023-06-30 10:58:47,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbaa4c81-1385-482c-8f11-90dd322df1b6/GCA_900764875.1_SRS259467_2_genomic.fna.gz --refList GCA_900764875.1_SRS259467_2_genomic.fna/target_genomes.txt --output GCA_900764875.1_SRS259467_2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:58:56,556] [INFO] Task succeeded: fastANI
[2023-06-30 10:58:56,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11657dd5-b5b1-4c14-a5f3-09c518198a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:58:56,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11657dd5-b5b1-4c14-a5f3-09c518198a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:58:56,569] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:58:56,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:58:56,570] [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 eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	94.6722	405	769	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	94.5229	409	769	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	94.4865	406	769	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	93.8584	438	769	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	93.858	433	769	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	93.7048	444	769	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	93.6984	440	769	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	91.501	403	769	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	88.863	347	769	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	83.5278	304	769	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	83.4586	310	769	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	83.1084	335	769	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	82.7678	312	769	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.1988	245	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:58:56,572] [INFO] DFAST Taxonomy check result was written to GCA_900764875.1_SRS259467_2_genomic.fna/tc_result.tsv
[2023-06-30 10:58:56,573] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:58:56,573] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:58:56,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11657dd5-b5b1-4c14-a5f3-09c518198a1d/dqc_reference/checkm_data
[2023-06-30 10:58:56,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:58:56,608] [INFO] Task started: CheckM
[2023-06-30 10:58:56,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900764875.1_SRS259467_2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900764875.1_SRS259467_2_genomic.fna/checkm_input GCA_900764875.1_SRS259467_2_genomic.fna/checkm_result
[2023-06-30 10:59:39,854] [INFO] Task succeeded: CheckM
[2023-06-30 10:59:39,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 10:59:39,878] [INFO] ===== Completeness check finished =====
[2023-06-30 10:59:39,878] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:59:39,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900764875.1_SRS259467_2_genomic.fna/markers.fasta)
[2023-06-30 10:59:39,879] [INFO] Task started: Blastn
[2023-06-30 10:59:39,879] [INFO] Running command: blastn -query GCA_900764875.1_SRS259467_2_genomic.fna/markers.fasta -db /var/lib/cwl/stg11657dd5-b5b1-4c14-a5f3-09c518198a1d/dqc_reference/reference_markers_gtdb.fasta -out GCA_900764875.1_SRS259467_2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:59:40,722] [INFO] Task succeeded: Blastn
[2023-06-30 10:59:40,727] [INFO] Selected 12 target genomes.
[2023-06-30 10:59:40,727] [INFO] Target genome list was writen to GCA_900764875.1_SRS259467_2_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:59:40,728] [INFO] Task started: fastANI
[2023-06-30 10:59:40,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbaa4c81-1385-482c-8f11-90dd322df1b6/GCA_900764875.1_SRS259467_2_genomic.fna.gz --refList GCA_900764875.1_SRS259467_2_genomic.fna/target_genomes_gtdb.txt --output GCA_900764875.1_SRS259467_2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:59:49,082] [INFO] Task succeeded: fastANI
[2023-06-30 10:59:49,097] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 10:59:49,097] [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_000155815.1	s__Bacteroides eggerthii	94.5229	409	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCF_000154205.1	s__Bacteroides uniformis	93.655	441	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_000614125.1	s__Bacteroides rodentium	89.6228	372	769	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	88.1943	346	769	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	85.7172	268	769	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	83.488	309	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_003438615.1	s__Bacteroides sp003545565	83.1032	334	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000154525.1	s__Bacteroides stercoris	82.7763	321	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_000374365.1	s__Bacteroides gallinarum	81.4598	308	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_902388495.1	s__Bacteroides sp902388495	80.3369	273	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000195635.1	s__Bacteroides fluxus	80.1695	284	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_000186225.1	s__Bacteroides helcogenes	79.2126	232	769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:59:49,099] [INFO] GTDB search result was written to GCA_900764875.1_SRS259467_2_genomic.fna/result_gtdb.tsv
[2023-06-30 10:59:49,100] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:59:49,104] [INFO] DFAST_QC result json was written to GCA_900764875.1_SRS259467_2_genomic.fna/dqc_result.json
[2023-06-30 10:59:49,104] [INFO] DFAST_QC completed!
[2023-06-30 10:59:49,104] [INFO] Total running time: 0h1m18s