[2024-01-24 13:25:47,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bab9f56-b734-4f8d-ae0a-06c6b53c2470/dqc_reference
[2024-01-24 13:25:48,653] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:48,654] [INFO] Task started: Prodigal
[2024-01-24 13:25:48,655] [INFO] Running command: gunzip -c /var/lib/cwl/stgd48a526d-7f87-481f-9304-ee265d3f3bee/GCF_900445515.1_53750_A01_genomic.fna.gz | prodigal -d GCF_900445515.1_53750_A01_genomic.fna/cds.fna -a GCF_900445515.1_53750_A01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:15,162] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:15,163] [INFO] Task started: HMMsearch
[2024-01-24 13:26:15,163] [INFO] Running command: hmmsearch --tblout GCF_900445515.1_53750_A01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bab9f56-b734-4f8d-ae0a-06c6b53c2470/dqc_reference/reference_markers.hmm GCF_900445515.1_53750_A01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:15,459] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:15,460] [INFO] Found 6/6 markers.
[2024-01-24 13:26:15,506] [INFO] Query marker FASTA was written to GCF_900445515.1_53750_A01_genomic.fna/markers.fasta
[2024-01-24 13:26:15,506] [INFO] Task started: Blastn
[2024-01-24 13:26:15,506] [INFO] Running command: blastn -query GCF_900445515.1_53750_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bab9f56-b734-4f8d-ae0a-06c6b53c2470/dqc_reference/reference_markers.fasta -out GCF_900445515.1_53750_A01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:16,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:16,132] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:16,132] [INFO] Target genome list was writen to GCF_900445515.1_53750_A01_genomic.fna/target_genomes.txt
[2024-01-24 13:26:16,137] [INFO] Task started: fastANI
[2024-01-24 13:26:16,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgd48a526d-7f87-481f-9304-ee265d3f3bee/GCF_900445515.1_53750_A01_genomic.fna.gz --refList GCF_900445515.1_53750_A01_genomic.fna/target_genomes.txt --output GCF_900445515.1_53750_A01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:27,026] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:27,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bab9f56-b734-4f8d-ae0a-06c6b53c2470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:27,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bab9f56-b734-4f8d-ae0a-06c6b53c2470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:27,038] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:26:27,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:27,038] [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 fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	100.0	1764	1769	95	conclusive
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	99.9967	1739	1769	95	conclusive
Bacteroides fragilis	strain=CCUG4856T	GCA_005706655.1	817	817	type	True	99.9955	1738	1769	95	conclusive
Bacteroides fragilis	strain=NCTC 9343	GCA_000025985.1	817	817	type	True	99.9941	1741	1769	95	conclusive
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	99.9894	1702	1769	95	conclusive
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	79.4177	348	1769	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	79.2349	405	1769	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	79.1168	360	1769	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	78.9767	372	1769	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	78.2497	274	1769	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:27,040] [INFO] DFAST Taxonomy check result was written to GCF_900445515.1_53750_A01_genomic.fna/tc_result.tsv
[2024-01-24 13:26:27,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:27,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:27,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bab9f56-b734-4f8d-ae0a-06c6b53c2470/dqc_reference/checkm_data
[2024-01-24 13:26:27,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:27,093] [INFO] Task started: CheckM
[2024-01-24 13:26:27,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445515.1_53750_A01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445515.1_53750_A01_genomic.fna/checkm_input GCF_900445515.1_53750_A01_genomic.fna/checkm_result
[2024-01-24 13:27:39,002] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:39,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:39,025] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:39,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:39,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445515.1_53750_A01_genomic.fna/markers.fasta)
[2024-01-24 13:27:39,026] [INFO] Task started: Blastn
[2024-01-24 13:27:39,026] [INFO] Running command: blastn -query GCF_900445515.1_53750_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bab9f56-b734-4f8d-ae0a-06c6b53c2470/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445515.1_53750_A01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:39,858] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:39,865] [INFO] Selected 18 target genomes.
[2024-01-24 13:27:39,865] [INFO] Target genome list was writen to GCF_900445515.1_53750_A01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:39,933] [INFO] Task started: fastANI
[2024-01-24 13:27:39,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgd48a526d-7f87-481f-9304-ee265d3f3bee/GCF_900445515.1_53750_A01_genomic.fna.gz --refList GCF_900445515.1_53750_A01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445515.1_53750_A01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:56,648] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:56,668] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:56,668] [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_000025985.1	s__Bacteroides fragilis	99.9941	1741	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	conclusive
GCF_002849695.1	s__Bacteroides fragilis_A	87.5582	1332	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	79.926	391	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_000381365.1	s__Bacteroides salyersiae	79.6561	427	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCA_014385165.1	s__Bacteroides sp014385165	79.4846	367	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	0.99	0.99	2	-
GCF_009193295.2	s__Bacteroides luhongzhouii	79.4637	362	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_001688725.2	s__Bacteroides caecimuris	79.44	351	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_900106755.1	s__Bacteroides faecis	79.4297	397	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCF_000210075.1	s__Bacteroides xylanisolvens	79.1117	375	1769	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	79.0792	408	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.55	98.11	0.85	0.80	13	-
GCF_001314995.1	s__Bacteroides ovatus	79.0177	372	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCA_000613385.1	s__Bacteroides acidifaciens	78.9642	337	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.33	97.99	0.81	0.75	18	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	78.9153	369	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCF_900130125.1	s__Bacteroides congonensis	78.776	397	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCA_902362375.1	s__Bacteroides sp902362375	78.741	376	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCA_900761785.1	s__Bacteroides sp900761785	78.3333	367	1769	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	78.0346	207	1769	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.84	99.84	0.94	0.94	2	-
GCA_900544675.1	s__Phocaeicola sp900544675	77.1967	105	1769	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 13:27:56,670] [INFO] GTDB search result was written to GCF_900445515.1_53750_A01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:56,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:56,674] [INFO] DFAST_QC result json was written to GCF_900445515.1_53750_A01_genomic.fna/dqc_result.json
[2024-01-24 13:27:56,674] [INFO] DFAST_QC completed!
[2024-01-24 13:27:56,674] [INFO] Total running time: 0h2m9s