[2024-01-24 12:45:20,757] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ad4788a-2be1-48ee-ad74-cbf0b0177c6c/dqc_reference
[2024-01-24 12:45:22,123] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:22,124] [INFO] Task started: Prodigal
[2024-01-24 12:45:22,124] [INFO] Running command: gunzip -c /var/lib/cwl/stge6f313fb-3f91-4e9a-9efe-8e7494f6da52/GCF_016696845.1_ASM1669684v1_genomic.fna.gz | prodigal -d GCF_016696845.1_ASM1669684v1_genomic.fna/cds.fna -a GCF_016696845.1_ASM1669684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:41,007] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:41,007] [INFO] Task started: HMMsearch
[2024-01-24 12:45:41,007] [INFO] Running command: hmmsearch --tblout GCF_016696845.1_ASM1669684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ad4788a-2be1-48ee-ad74-cbf0b0177c6c/dqc_reference/reference_markers.hmm GCF_016696845.1_ASM1669684v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:41,286] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:41,287] [INFO] Found 6/6 markers.
[2024-01-24 12:45:41,316] [INFO] Query marker FASTA was written to GCF_016696845.1_ASM1669684v1_genomic.fna/markers.fasta
[2024-01-24 12:45:41,317] [INFO] Task started: Blastn
[2024-01-24 12:45:41,317] [INFO] Running command: blastn -query GCF_016696845.1_ASM1669684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad4788a-2be1-48ee-ad74-cbf0b0177c6c/dqc_reference/reference_markers.fasta -out GCF_016696845.1_ASM1669684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:41,926] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:41,933] [INFO] Selected 9 target genomes.
[2024-01-24 12:45:41,934] [INFO] Target genome list was writen to GCF_016696845.1_ASM1669684v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:41,941] [INFO] Task started: fastANI
[2024-01-24 12:45:41,941] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f313fb-3f91-4e9a-9efe-8e7494f6da52/GCF_016696845.1_ASM1669684v1_genomic.fna.gz --refList GCF_016696845.1_ASM1669684v1_genomic.fna/target_genomes.txt --output GCF_016696845.1_ASM1669684v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:50,289] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:50,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ad4788a-2be1-48ee-ad74-cbf0b0177c6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:50,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ad4788a-2be1-48ee-ad74-cbf0b0177c6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:50,296] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:45:50,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:50,297] [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
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	100.0	1099	1102	95	conclusive
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	100.0	1100	1102	95	conclusive
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	99.9943	1097	1102	95	conclusive
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	82.4339	143	1102	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	82.3598	149	1102	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	80.6418	214	1102	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	79.1184	132	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:50,298] [INFO] DFAST Taxonomy check result was written to GCF_016696845.1_ASM1669684v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:50,299] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:50,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:50,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ad4788a-2be1-48ee-ad74-cbf0b0177c6c/dqc_reference/checkm_data
[2024-01-24 12:45:50,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:50,338] [INFO] Task started: CheckM
[2024-01-24 12:45:50,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016696845.1_ASM1669684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016696845.1_ASM1669684v1_genomic.fna/checkm_input GCF_016696845.1_ASM1669684v1_genomic.fna/checkm_result
[2024-01-24 12:46:44,694] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:44,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:44,716] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:44,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:44,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016696845.1_ASM1669684v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:44,717] [INFO] Task started: Blastn
[2024-01-24 12:46:44,718] [INFO] Running command: blastn -query GCF_016696845.1_ASM1669684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad4788a-2be1-48ee-ad74-cbf0b0177c6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016696845.1_ASM1669684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:45,568] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:45,576] [INFO] Selected 23 target genomes.
[2024-01-24 12:46:45,576] [INFO] Target genome list was writen to GCF_016696845.1_ASM1669684v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:45,610] [INFO] Task started: fastANI
[2024-01-24 12:46:45,610] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f313fb-3f91-4e9a-9efe-8e7494f6da52/GCF_016696845.1_ASM1669684v1_genomic.fna.gz --refList GCF_016696845.1_ASM1669684v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016696845.1_ASM1669684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:57,513] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:57,535] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:57,535] [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_002201515.1	s__Muribaculum intestinale	100.0	1098	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.09	97.90	0.92	0.80	20	conclusive
GCF_004803915.1	s__Duncaniella dubosii	82.7147	146	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.46	96.11	0.91	0.80	8	-
GCF_004803695.1	s__Muribaculum gordoncarteri	80.4902	214	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	96.82	95.63	0.92	0.83	15	-
GCA_004102785.1	s__UBA7173 sp002491305	80.228	155	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.18	98.68	0.94	0.92	6	-
GCA_910583865.1	s__Muribaculum sp910583865	79.6763	424	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004102805.1	s__UBA7173 sp004102805	79.3276	153	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.86	98.86	0.92	0.89	3	-
GCA_905193485.1	s__Paramuribaculum sp905193485	77.8122	76	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578835.1	s__Muribaculum sp910578835	77.7557	171	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587665.1	s__Muribaculum sp910587665	77.7089	132	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689445.1	s__M3 sp001689445	77.5853	125	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__M3	95.0	99.97	99.97	0.98	0.98	2	-
GCA_003150235.1	s__Muribaculum sp003150235	77.5836	166	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.90	96.97	0.85	0.80	6	-
GCA_009775605.1	s__Paramuribaculum sp009775605	77.5762	115	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	99.73	99.73	0.91	0.91	2	-
GCA_910578785.1	s__Muribaculum sp910578785	77.5327	149	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584825.1	s__Duncaniella sp910584825	77.4907	140	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775095.1	s__Muribaculum sp009775095	77.4305	151	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.95	99.95	0.97	0.97	2	-
GCA_001689405.1	s__Muribaculum arabinoxylanisolvens	77.3659	155	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.46	99.01	0.94	0.92	3	-
GCA_905210435.1	s__UBA7173 sp905210435	77.2929	133	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801485.1	s__CAG-873 sp014801485	77.2497	79	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001915385.1	s__UBA7173 sp001915385	77.2396	130	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	96.67	96.43	0.78	0.73	4	-
GCA_009177195.1	s__Muribaculum sp009177195	77.1351	93	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541865.1	s__CAG-873 sp900541865	77.0411	78	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586995.1	s__CAG-873 sp910586995	76.9137	82	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587075.1	s__UBA7173 sp910587075	76.8759	97	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:57,536] [INFO] GTDB search result was written to GCF_016696845.1_ASM1669684v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:57,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:57,540] [INFO] DFAST_QC result json was written to GCF_016696845.1_ASM1669684v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:57,540] [INFO] DFAST_QC completed!
[2024-01-24 12:46:57,541] [INFO] Total running time: 0h1m37s