[2024-01-25 20:00:35,368] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:35,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:35,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg649d6802-482d-4908-b26d-550005e64cea/dqc_reference
[2024-01-25 20:00:36,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:36,497] [INFO] Task started: Prodigal
[2024-01-25 20:00:36,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg756e3538-186c-463b-8095-f0f84d6b5721/GCF_024609215.1_ASM2460921v3_genomic.fna.gz | prodigal -d GCF_024609215.1_ASM2460921v3_genomic.fna/cds.fna -a GCF_024609215.1_ASM2460921v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:43,482] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:43,483] [INFO] Task started: HMMsearch
[2024-01-25 20:00:43,483] [INFO] Running command: hmmsearch --tblout GCF_024609215.1_ASM2460921v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg649d6802-482d-4908-b26d-550005e64cea/dqc_reference/reference_markers.hmm GCF_024609215.1_ASM2460921v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:43,668] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:43,669] [INFO] Found 6/6 markers.
[2024-01-25 20:00:43,694] [INFO] Query marker FASTA was written to GCF_024609215.1_ASM2460921v3_genomic.fna/markers.fasta
[2024-01-25 20:00:43,694] [INFO] Task started: Blastn
[2024-01-25 20:00:43,695] [INFO] Running command: blastn -query GCF_024609215.1_ASM2460921v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg649d6802-482d-4908-b26d-550005e64cea/dqc_reference/reference_markers.fasta -out GCF_024609215.1_ASM2460921v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:44,336] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:44,339] [INFO] Selected 23 target genomes.
[2024-01-25 20:00:44,340] [INFO] Target genome list was writen to GCF_024609215.1_ASM2460921v3_genomic.fna/target_genomes.txt
[2024-01-25 20:00:44,353] [INFO] Task started: fastANI
[2024-01-25 20:00:44,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg756e3538-186c-463b-8095-f0f84d6b5721/GCF_024609215.1_ASM2460921v3_genomic.fna.gz --refList GCF_024609215.1_ASM2460921v3_genomic.fna/target_genomes.txt --output GCF_024609215.1_ASM2460921v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:58,859] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:58,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg649d6802-482d-4908-b26d-550005e64cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:58,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg649d6802-482d-4908-b26d-550005e64cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:58,872] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:00:58,872] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:00:58,872] [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
Denitrobacterium detoxificans	strain=NPOH1	GCA_001643775.1	79604	79604	type	True	78.0401	165	810	95	below_threshold
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	77.8946	111	810	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	77.879	184	810	95	below_threshold
Denitrobacterium detoxificans	strain=DSM 21843	GCA_900110565.1	79604	79604	type	True	77.8744	166	810	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	77.8176	181	810	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	77.8097	182	810	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	77.5677	181	810	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	77.5665	174	810	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	77.5607	175	810	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	77.5513	177	810	95	below_threshold
Berryella intestinalis	strain=68-1-3	GCA_000814825.1	1531429	1531429	type	True	77.5509	115	810	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	77.5485	168	810	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	77.4757	138	810	95	below_threshold
Adlercreutzia caecimuris	strain=DSM 21839	GCA_024623275.1	671266	671266	type	True	77.4383	126	810	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_024623245.1	1796610	1796610	type	True	77.3508	124	810	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_008831045.1	1796610	1796610	type	True	77.3227	120	810	95	below_threshold
Adlercreutzia mucosicola	strain=DSM 19490	GCA_000422625.1	580026	580026	type	True	77.2788	134	810	95	below_threshold
Adlercreutzia mucosicola	strain=DSM 19490	GCA_024623255.1	580026	580026	type	True	77.2677	127	810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:58,875] [INFO] DFAST Taxonomy check result was written to GCF_024609215.1_ASM2460921v3_genomic.fna/tc_result.tsv
[2024-01-25 20:00:58,876] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:58,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:58,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg649d6802-482d-4908-b26d-550005e64cea/dqc_reference/checkm_data
[2024-01-25 20:00:58,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:58,904] [INFO] Task started: CheckM
[2024-01-25 20:00:58,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024609215.1_ASM2460921v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024609215.1_ASM2460921v3_genomic.fna/checkm_input GCF_024609215.1_ASM2460921v3_genomic.fna/checkm_result
[2024-01-25 20:01:22,845] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:22,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:22,869] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:22,869] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:22,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024609215.1_ASM2460921v3_genomic.fna/markers.fasta)
[2024-01-25 20:01:22,870] [INFO] Task started: Blastn
[2024-01-25 20:01:22,870] [INFO] Running command: blastn -query GCF_024609215.1_ASM2460921v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg649d6802-482d-4908-b26d-550005e64cea/dqc_reference/reference_markers_gtdb.fasta -out GCF_024609215.1_ASM2460921v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:23,961] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:23,963] [INFO] Selected 24 target genomes.
[2024-01-25 20:01:23,964] [INFO] Target genome list was writen to GCF_024609215.1_ASM2460921v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:23,997] [INFO] Task started: fastANI
[2024-01-25 20:01:23,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg756e3538-186c-463b-8095-f0f84d6b5721/GCF_024609215.1_ASM2460921v3_genomic.fna.gz --refList GCF_024609215.1_ASM2460921v3_genomic.fna/target_genomes_gtdb.txt --output GCF_024609215.1_ASM2460921v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:33,548] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:33,562] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:01:33,562] [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
GCA_905236045.1	s__Denitrobacterium sp905236045	79.1849	203	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Denitrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001486445.1	s__RUG013 sp001486445	78.1692	157	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RUG013	95.0	98.36	97.63	0.92	0.89	7	-
GCA_015062615.1	s__Denitrobacterium detoxificans_A	78.0515	165	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Denitrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001643775.1	s__Denitrobacterium detoxificans	78.0401	165	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Denitrobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013185065.1	s__CAAEEV01 sp013185065	78.0042	163	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
GCF_003725295.1	s__Slackia_A faecicanis	77.8946	111	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199375.1	s__Gordonibacter urolithinfaciens	77.8554	179	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
GCA_015062635.1	s__UMGS1519 sp015062635	77.8501	110	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UMGS1519	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550385.1	s__Aphodovivens sp900550385	77.8385	144	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	99.66	99.66	0.86	0.86	2	-
GCA_900754495.1	s__Aphodovivens avicola	77.7782	120	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	96.28	95.91	0.79	0.73	3	-
GCF_011038975.1	s__CAAEEV01 sp011038975	77.7543	171	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.99	99.99	0.98	0.98	2	-
GCA_910589695.1	s__QWKK01 sp910589695	77.6202	120	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339815.1	s__Eggerthella sinensis	77.5485	168	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCA_910589165.1	s__Adlercreutzia sp910589165	77.4131	144	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715725.1	s__Aveggerthella excrementigallinarum	77.405	127	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aveggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754955.1	s__CAAEEV01 sp900754955	77.2608	115	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.85	99.85	0.86	0.86	2	-
GCA_017440565.1	s__RGIG3135 sp017440565	77.2601	101	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RGIG3135	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767025.1	s__CACXMZ01 sp902767025	77.2465	91	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CACXMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768975.1	s__CACXMZ01 sp902768975	77.0238	57	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CACXMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900315.1	s__Thermophilibacter profusa_A	76.9809	81	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420575.1	s__CAJFUR01 sp904420575	76.8352	120	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAJFUR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314495.1	s__UBA7741 sp900314495	76.7597	59	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	98.85	98.57	0.91	0.87	9	-
GCA_904420215.1	s__CAJFUR01 sp904420215	76.6277	125	810	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAJFUR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:33,563] [INFO] GTDB search result was written to GCF_024609215.1_ASM2460921v3_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:33,564] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:33,570] [INFO] DFAST_QC result json was written to GCF_024609215.1_ASM2460921v3_genomic.fna/dqc_result.json
[2024-01-25 20:01:33,570] [INFO] DFAST_QC completed!
[2024-01-25 20:01:33,570] [INFO] Total running time: 0h0m58s