[2024-01-24 13:58:10,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,289] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg8555bafb-6205-4f50-b374-2522f519a27e/dqc_reference
[2024-01-24 13:58:11,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,395] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,395] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0978a8e-8bd8-4cac-a889-9150e2219dff/GCF_004803695.1_ASM480369v1_genomic.fna.gz | prodigal -d GCF_004803695.1_ASM480369v1_genomic.fna/cds.fna -a GCF_004803695.1_ASM480369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:27,237] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:27,238] [INFO] Task started: HMMsearch
[2024-01-24 13:58:27,238] [INFO] Running command: hmmsearch --tblout GCF_004803695.1_ASM480369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8555bafb-6205-4f50-b374-2522f519a27e/dqc_reference/reference_markers.hmm GCF_004803695.1_ASM480369v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:27,446] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:27,447] [INFO] Found 6/6 markers.
[2024-01-24 13:58:27,472] [INFO] Query marker FASTA was written to GCF_004803695.1_ASM480369v1_genomic.fna/markers.fasta
[2024-01-24 13:58:27,472] [INFO] Task started: Blastn
[2024-01-24 13:58:27,472] [INFO] Running command: blastn -query GCF_004803695.1_ASM480369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8555bafb-6205-4f50-b374-2522f519a27e/dqc_reference/reference_markers.fasta -out GCF_004803695.1_ASM480369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:28,002] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:28,005] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:28,005] [INFO] Target genome list was writen to GCF_004803695.1_ASM480369v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:28,018] [INFO] Task started: fastANI
[2024-01-24 13:58:28,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0978a8e-8bd8-4cac-a889-9150e2219dff/GCF_004803695.1_ASM480369v1_genomic.fna.gz --refList GCF_004803695.1_ASM480369v1_genomic.fna/target_genomes.txt --output GCF_004803695.1_ASM480369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:36,281] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:36,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8555bafb-6205-4f50-b374-2522f519a27e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:36,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8555bafb-6205-4f50-b374-2522f519a27e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:36,289] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:36,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:36,289] [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 gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	100.0	1128	1142	95	conclusive
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	84.922	172	1142	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	80.9116	158	1142	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	80.6867	211	1142	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	80.563	213	1142	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	80.3333	211	1142	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	79.5586	140	1142	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	78.7433	235	1142	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	77.4172	69	1142	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	76.5531	69	1142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,290] [INFO] DFAST Taxonomy check result was written to GCF_004803695.1_ASM480369v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:36,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:36,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:36,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8555bafb-6205-4f50-b374-2522f519a27e/dqc_reference/checkm_data
[2024-01-24 13:58:36,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:36,326] [INFO] Task started: CheckM
[2024-01-24 13:58:36,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004803695.1_ASM480369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004803695.1_ASM480369v1_genomic.fna/checkm_input GCF_004803695.1_ASM480369v1_genomic.fna/checkm_result
[2024-01-24 13:59:22,470] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:22,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:22,485] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:22,485] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:22,485] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004803695.1_ASM480369v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:22,485] [INFO] Task started: Blastn
[2024-01-24 13:59:22,485] [INFO] Running command: blastn -query GCF_004803695.1_ASM480369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8555bafb-6205-4f50-b374-2522f519a27e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004803695.1_ASM480369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:23,308] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:23,311] [INFO] Selected 23 target genomes.
[2024-01-24 13:59:23,311] [INFO] Target genome list was writen to GCF_004803695.1_ASM480369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:23,322] [INFO] Task started: fastANI
[2024-01-24 13:59:23,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0978a8e-8bd8-4cac-a889-9150e2219dff/GCF_004803695.1_ASM480369v1_genomic.fna.gz --refList GCF_004803695.1_ASM480369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004803695.1_ASM480369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:35,609] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:35,622] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:35,622] [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_004803695.1	s__Muribaculum gordoncarteri	100.0	1134	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	96.82	95.63	0.92	0.83	15	conclusive
GCF_002201515.1	s__Muribaculum intestinale	80.5619	209	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.09	97.90	0.92	0.80	20	-
GCA_001689405.1	s__Muribaculum arabinoxylanisolvens	78.8454	266	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.46	99.01	0.94	0.92	3	-
GCF_008728965.1	s__Muribaculum faecis	78.7433	235	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.62	99.32	0.94	0.91	9	-
GCA_910578835.1	s__Muribaculum sp910578835	78.5312	239	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570975.1	s__Muribaculum sp001701195	78.5085	260	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.86	97.86	0.92	0.92	2	-
GCA_003150235.1	s__Muribaculum sp003150235	78.383	254	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.90	96.97	0.85	0.80	6	-
GCA_910587665.1	s__Muribaculum sp910587665	78.2193	232	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001701065.1	s__Muribaculum sp001701065	78.1031	188	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775095.1	s__Muribaculum sp009775095	78.0651	259	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.95	99.95	0.97	0.97	2	-
GCA_014801525.1	s__Muribaculum sp014801525	77.8044	121	1142	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	77.7959	183	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__M3	95.0	99.97	99.97	0.98	0.98	2	-
GCF_009676955.1	s__Sodaliphilus pleomorphus	77.6985	70	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.46	98.06	0.93	0.87	18	-
GCA_910578785.1	s__Muribaculum sp910578785	77.6504	223	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762315.1	s__Duncaniella sp900762315	77.3757	163	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584825.1	s__Duncaniella sp910584825	77.3422	150	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583865.1	s__Muribaculum sp910583865	77.275	152	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577465.1	s__Paramuribaculum sp910577465	77.2279	97	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551515.1	s__Paramuribaculum sp900551515	77.1481	96	1142	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	77.018	81	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.33	0.87	0.87	2	-
GCA_910587475.1	s__CAG-873 sp910587475	76.982	88	1142	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_017462345.1	s__RGIG4079 sp017462345	76.9674	79	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__RGIG4079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014800605.1	s__UBA7173 sp014800605	76.8452	71	1142	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 13:59:35,623] [INFO] GTDB search result was written to GCF_004803695.1_ASM480369v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:35,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:35,626] [INFO] DFAST_QC result json was written to GCF_004803695.1_ASM480369v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:35,626] [INFO] DFAST_QC completed!
[2024-01-24 13:59:35,626] [INFO] Total running time: 0h1m25s