[2024-01-24 13:37:26,183] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:26,185] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:26,186] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1174220-09a0-4793-86b1-708fbb00548a/dqc_reference
[2024-01-24 13:37:27,336] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,337] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg6019ef1f-c877-4e04-b881-05eab9d290c4/GCF_014288095.1_ASM1428809v1_genomic.fna.gz | prodigal -d GCF_014288095.1_ASM1428809v1_genomic.fna/cds.fna -a GCF_014288095.1_ASM1428809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:48,050] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:48,050] [INFO] Task started: HMMsearch
[2024-01-24 13:37:48,050] [INFO] Running command: hmmsearch --tblout GCF_014288095.1_ASM1428809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1174220-09a0-4793-86b1-708fbb00548a/dqc_reference/reference_markers.hmm GCF_014288095.1_ASM1428809v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:48,322] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:48,323] [INFO] Found 6/6 markers.
[2024-01-24 13:37:48,360] [INFO] Query marker FASTA was written to GCF_014288095.1_ASM1428809v1_genomic.fna/markers.fasta
[2024-01-24 13:37:48,361] [INFO] Task started: Blastn
[2024-01-24 13:37:48,361] [INFO] Running command: blastn -query GCF_014288095.1_ASM1428809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1174220-09a0-4793-86b1-708fbb00548a/dqc_reference/reference_markers.fasta -out GCF_014288095.1_ASM1428809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:48,940] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:48,943] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:48,943] [INFO] Target genome list was writen to GCF_014288095.1_ASM1428809v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:48,947] [INFO] Task started: fastANI
[2024-01-24 13:37:48,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg6019ef1f-c877-4e04-b881-05eab9d290c4/GCF_014288095.1_ASM1428809v1_genomic.fna.gz --refList GCF_014288095.1_ASM1428809v1_genomic.fna/target_genomes.txt --output GCF_014288095.1_ASM1428809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:59,619] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:59,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1174220-09a0-4793-86b1-708fbb00548a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:59,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1174220-09a0-4793-86b1-708fbb00548a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:59,627] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:59,628] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:59,628] [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 fragilis	strain=NCTC 9343	GCA_000025985.1	817	817	type	True	87.0227	1275	1681	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	86.9801	1262	1681	95	below_threshold
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	86.9685	1269	1681	95	below_threshold
Bacteroides fragilis	strain=CCUG4856T	GCA_005706655.1	817	817	type	True	86.9654	1269	1681	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	86.938	1278	1681	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	79.2151	406	1681	95	below_threshold
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	79.0745	432	1681	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	78.743	353	1681	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	78.7303	378	1681	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	78.6258	375	1681	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:59,629] [INFO] DFAST Taxonomy check result was written to GCF_014288095.1_ASM1428809v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:59,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:59,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:59,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1174220-09a0-4793-86b1-708fbb00548a/dqc_reference/checkm_data
[2024-01-24 13:37:59,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:59,678] [INFO] Task started: CheckM
[2024-01-24 13:37:59,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014288095.1_ASM1428809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014288095.1_ASM1428809v1_genomic.fna/checkm_input GCF_014288095.1_ASM1428809v1_genomic.fna/checkm_result
[2024-01-24 13:38:56,793] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:56,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:56,809] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:56,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:56,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014288095.1_ASM1428809v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:56,810] [INFO] Task started: Blastn
[2024-01-24 13:38:56,810] [INFO] Running command: blastn -query GCF_014288095.1_ASM1428809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1174220-09a0-4793-86b1-708fbb00548a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014288095.1_ASM1428809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:57,696] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:57,699] [INFO] Selected 21 target genomes.
[2024-01-24 13:38:57,699] [INFO] Target genome list was writen to GCF_014288095.1_ASM1428809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:57,732] [INFO] Task started: fastANI
[2024-01-24 13:38:57,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg6019ef1f-c877-4e04-b881-05eab9d290c4/GCF_014288095.1_ASM1428809v1_genomic.fna.gz --refList GCF_014288095.1_ASM1428809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014288095.1_ASM1428809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:17,339] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:17,351] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:17,351] [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_002849695.1	s__Bacteroides fragilis_A	98.3777	1433	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	conclusive
GCF_000025985.1	s__Bacteroides fragilis	87.0314	1273	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	-
GCF_000381365.1	s__Bacteroides salyersiae	79.3826	395	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	79.1812	402	1681	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	79.1389	390	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_000210075.1	s__Bacteroides xylanisolvens	79.0701	367	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCA_000613465.1	s__Bacteroides nordii	79.0429	419	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.55	98.11	0.85	0.80	13	-
GCF_012113595.1	s__Bacteroides sp012113595	78.9254	405	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903181435.1	s__Bacteroides sp900765785	78.8208	348	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_001314995.1	s__Bacteroides ovatus	78.8028	372	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCA_902362375.1	s__Bacteroides sp902362375	78.7032	387	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCA_014385165.1	s__Bacteroides sp014385165	78.6731	351	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	0.99	0.99	2	-
GCF_002222615.2	s__Bacteroides caccae	78.6101	377	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCA_905207245.1	s__Bacteroides sp905207245	78.3688	305	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315485.1	s__Bacteroides oleiciplenus	78.2739	317	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.39	98.79	0.93	0.86	3	-
GCF_003464595.1	s__Bacteroides intestinalis_A	78.2064	307	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	97.86	96.66	0.85	0.74	7	-
GCA_900762525.1	s__Bacteroides sp900762525	78.1805	332	1681	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	78.0442	365	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215555.1	s__Bacteroides sp905215555	77.5957	247	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544675.1	s__Phocaeicola sp900544675	77.0926	103	1681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.98	99.96	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:17,353] [INFO] GTDB search result was written to GCF_014288095.1_ASM1428809v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:17,354] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:17,357] [INFO] DFAST_QC result json was written to GCF_014288095.1_ASM1428809v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:17,357] [INFO] DFAST_QC completed!
[2024-01-24 13:39:17,357] [INFO] Total running time: 0h1m51s