[2024-01-24 12:28:34,798] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg5439a110-6098-4f95-a106-2a0b4d371cbe/dqc_reference
[2024-01-24 12:28:36,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:36,007] [INFO] Task started: Prodigal
[2024-01-24 12:28:36,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ede00b4-69cc-443d-83b5-37bfb465d3c9/GCF_003024925.1_ASM302492v1_genomic.fna.gz | prodigal -d GCF_003024925.1_ASM302492v1_genomic.fna/cds.fna -a GCF_003024925.1_ASM302492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:51,212] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:51,213] [INFO] Task started: HMMsearch
[2024-01-24 12:28:51,213] [INFO] Running command: hmmsearch --tblout GCF_003024925.1_ASM302492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5439a110-6098-4f95-a106-2a0b4d371cbe/dqc_reference/reference_markers.hmm GCF_003024925.1_ASM302492v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:51,457] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:51,458] [INFO] Found 6/6 markers.
[2024-01-24 12:28:51,522] [INFO] Query marker FASTA was written to GCF_003024925.1_ASM302492v1_genomic.fna/markers.fasta
[2024-01-24 12:28:51,523] [INFO] Task started: Blastn
[2024-01-24 12:28:51,523] [INFO] Running command: blastn -query GCF_003024925.1_ASM302492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5439a110-6098-4f95-a106-2a0b4d371cbe/dqc_reference/reference_markers.fasta -out GCF_003024925.1_ASM302492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:52,110] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:52,113] [INFO] Selected 19 target genomes.
[2024-01-24 12:28:52,114] [INFO] Target genome list was writen to GCF_003024925.1_ASM302492v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:52,157] [INFO] Task started: fastANI
[2024-01-24 12:28:52,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ede00b4-69cc-443d-83b5-37bfb465d3c9/GCF_003024925.1_ASM302492v1_genomic.fna.gz --refList GCF_003024925.1_ASM302492v1_genomic.fna/target_genomes.txt --output GCF_003024925.1_ASM302492v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:03,552] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:03,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5439a110-6098-4f95-a106-2a0b4d371cbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:03,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5439a110-6098-4f95-a106-2a0b4d371cbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:03,565] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:03,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:03,566] [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
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	100.0	744	757	95	conclusive
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	79.2963	127	757	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	79.2526	124	757	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	79.2064	128	757	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	79.1535	111	757	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	79.0096	105	757	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	78.6674	134	757	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:03,567] [INFO] DFAST Taxonomy check result was written to GCF_003024925.1_ASM302492v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:03,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:03,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:03,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5439a110-6098-4f95-a106-2a0b4d371cbe/dqc_reference/checkm_data
[2024-01-24 12:29:03,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:03,602] [INFO] Task started: CheckM
[2024-01-24 12:29:03,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024925.1_ASM302492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024925.1_ASM302492v1_genomic.fna/checkm_input GCF_003024925.1_ASM302492v1_genomic.fna/checkm_result
[2024-01-24 12:29:49,976] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:49,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:50,001] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:50,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:50,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024925.1_ASM302492v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:50,002] [INFO] Task started: Blastn
[2024-01-24 12:29:50,002] [INFO] Running command: blastn -query GCF_003024925.1_ASM302492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5439a110-6098-4f95-a106-2a0b4d371cbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024925.1_ASM302492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:50,895] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:50,900] [INFO] Selected 23 target genomes.
[2024-01-24 12:29:50,900] [INFO] Target genome list was writen to GCF_003024925.1_ASM302492v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:50,965] [INFO] Task started: fastANI
[2024-01-24 12:29:50,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ede00b4-69cc-443d-83b5-37bfb465d3c9/GCF_003024925.1_ASM302492v1_genomic.fna.gz --refList GCF_003024925.1_ASM302492v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003024925.1_ASM302492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:09,578] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:09,600] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:09,600] [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_003024925.1	s__Paramuribaculum intestinale	100.0	744	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	99.05	97.83	0.86	0.82	16	conclusive
GCA_003762715.1	s__Paramuribaculum sp001689565	80.7897	152	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.89	98.71	0.85	0.83	3	-
GCF_002201515.1	s__Muribaculum intestinale	79.3156	127	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.09	97.90	0.92	0.80	20	-
GCA_004102805.1	s__UBA7173 sp004102805	79.0442	115	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.86	98.86	0.92	0.89	3	-
GCA_910576785.1	s__Duncaniella sp910576785	77.9859	107	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689535.1	s__Paramuribaculum sp001689535	77.9738	120	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.63	98.52	0.86	0.84	5	-
GCA_009775605.1	s__Paramuribaculum sp009775605	77.9603	121	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	99.73	99.73	0.91	0.91	2	-
GCA_014802045.1	s__Paramuribaculum sp014802045	77.8194	146	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.51	98.31	0.80	0.73	3	-
GCA_910587425.1	s__Paramuribaculum sp910587425	77.6562	171	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579675.1	s__Paramuribaculum sp910579675	77.6132	153	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689495.1	s__Duncaniella sp001689495	77.4319	153	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	99.23	99.23	0.93	0.93	2	-
GCA_009775095.1	s__Muribaculum sp009775095	77.3888	68	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.95	99.95	0.97	0.97	2	-
GCA_910578095.1	s__CAG-873 sp910578095	77.3753	88	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.96	99.96	0.98	0.98	2	-
GCA_900546365.1	s__Paramuribaculum sp900546365	77.3688	104	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210435.1	s__UBA7173 sp905210435	77.2906	117	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689445.1	s__M3 sp001689445	77.1976	107	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__M3	95.0	99.97	99.97	0.98	0.98	2	-
GCA_910586665.1	s__Duncaniella sp910586665	77.1779	99	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579105.1	s__UBA7173 sp910579105	77.1561	79	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621225.1	s__Paramuribaculum sp017621225	77.0007	95	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759915.1	s__Paramuribaculum sp900759915	76.9265	98	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.33	0.87	0.87	2	-
GCA_910586475.1	s__Paramuribaculum sp910586475	76.5923	72	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002494015.1	s__Duncaniella sp002494015	76.5816	79	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	99.82	98.87	0.95	0.90	8	-
GCA_910589055.1	s__CAG-873 sp910589055	76.5347	81	757	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:09,602] [INFO] GTDB search result was written to GCF_003024925.1_ASM302492v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:09,603] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:09,606] [INFO] DFAST_QC result json was written to GCF_003024925.1_ASM302492v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:09,606] [INFO] DFAST_QC completed!
[2024-01-24 12:30:09,607] [INFO] Total running time: 0h1m35s