[2023-06-05 10:46:57,383] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:46:57,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:46:57,397] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd705444-82d6-4046-abfd-418c0ef39add/dqc_reference
[2023-06-05 10:46:59,023] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:46:59,024] [INFO] Task started: Prodigal
[2023-06-05 10:46:59,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg282ee28b-4075-47c9-83a2-46ef5afbe2ea/GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna.gz | prodigal -d GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/cds.fna -a GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:47:03,791] [INFO] Task succeeded: Prodigal
[2023-06-05 10:47:03,792] [INFO] Task started: HMMsearch
[2023-06-05 10:47:03,792] [INFO] Running command: hmmsearch --tblout GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd705444-82d6-4046-abfd-418c0ef39add/dqc_reference/reference_markers.hmm GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:47:04,001] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:47:04,002] [INFO] Found 6/6 markers.
[2023-06-05 10:47:04,041] [INFO] Query marker FASTA was written to GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/markers.fasta
[2023-06-05 10:47:04,042] [INFO] Task started: Blastn
[2023-06-05 10:47:04,042] [INFO] Running command: blastn -query GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd705444-82d6-4046-abfd-418c0ef39add/dqc_reference/reference_markers.fasta -out GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:04,663] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:04,666] [INFO] Selected 19 target genomes.
[2023-06-05 10:47:04,667] [INFO] Target genome list was writen to GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/target_genomes.txt
[2023-06-05 10:47:04,673] [INFO] Task started: fastANI
[2023-06-05 10:47:04,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg282ee28b-4075-47c9-83a2-46ef5afbe2ea/GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna.gz --refList GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/target_genomes.txt --output GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:47:13,828] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:13,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd705444-82d6-4046-abfd-418c0ef39add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:47:13,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd705444-82d6-4046-abfd-418c0ef39add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:47:13,838] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:47:13,838] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:47:13,838] [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
Xiamenia xianingshaonis	strain=zg-886	GCA_017945865.1	2682776	2682776	type	True	78.3128	56	457	95	below_threshold
Xiamenia xianingshaonis	strain=zg-886	GCA_011392455.1	2682776	2682776	type	True	78.1763	59	457	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	78.0711	87	457	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	77.9111	77	457	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	77.8836	79	457	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	77.8589	80	457	95	below_threshold
Berryella intestinalis	strain=68-1-3	GCA_000814825.1	1531429	1531429	type	True	77.8477	71	457	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	77.8283	77	457	95	below_threshold
Adlercreutzia mucosicola	strain=DSM 19490	GCA_024623255.1	580026	580026	type	True	77.5659	62	457	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_008831045.1	1796610	1796610	type	True	77.4143	57	457	95	below_threshold
Senegalimassilia faecalis	strain=KGMB04484	GCA_004135645.1	2509433	2509433	type	True	77.3885	66	457	95	below_threshold
Raoultibacter timonensis	strain=Marseille-P3277	GCA_900240215.1	1907662	1907662	type	True	77.3518	65	457	95	below_threshold
Slackia exigua	strain=NCTC12994	GCA_900450505.1	84109	84109	type	True	77.203	52	457	95	below_threshold
Slackia exigua	strain=ATCC 700122	GCA_000162875.1	84109	84109	type	True	77.1533	53	457	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:47:13,840] [INFO] DFAST Taxonomy check result was written to GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/tc_result.tsv
[2023-06-05 10:47:13,840] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:47:13,840] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:47:13,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd705444-82d6-4046-abfd-418c0ef39add/dqc_reference/checkm_data
[2023-06-05 10:47:13,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:47:13,864] [INFO] Task started: CheckM
[2023-06-05 10:47:13,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/checkm_input GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/checkm_result
[2023-06-05 10:47:33,084] [INFO] Task succeeded: CheckM
[2023-06-05 10:47:33,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:47:33,105] [INFO] ===== Completeness check finished =====
[2023-06-05 10:47:33,106] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:47:33,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/markers.fasta)
[2023-06-05 10:47:33,107] [INFO] Task started: Blastn
[2023-06-05 10:47:33,107] [INFO] Running command: blastn -query GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd705444-82d6-4046-abfd-418c0ef39add/dqc_reference/reference_markers_gtdb.fasta -out GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:34,001] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:34,005] [INFO] Selected 13 target genomes.
[2023-06-05 10:47:34,005] [INFO] Target genome list was writen to GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:47:34,064] [INFO] Task started: fastANI
[2023-06-05 10:47:34,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg282ee28b-4075-47c9-83a2-46ef5afbe2ea/GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna.gz --refList GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/target_genomes_gtdb.txt --output GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:47:39,863] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:39,871] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:47:39,872] [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_902779135.1	s__UBA9715 sp902779135	96.357	381	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	96.17	95.88	0.78	0.73	4	conclusive
GCA_902781245.1	s__UBA9715 sp902781245	92.4723	295	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432445.1	s__UBA9715 sp017432445	80.3712	184	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371495.1	s__UBA9715 sp002371495	80.0774	186	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902764575.1	s__UBA9715 sp902764575	80.029	188	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017434045.1	s__UBA9715 sp017434045	80.0234	142	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234785.1	s__UBA9715 sp905234785	79.9566	183	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788545.1	s__UBA9715 sp902788545	79.9377	153	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017459925.1	s__UBA9715 sp017459925	79.6976	188	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017511465.1	s__UBA9715 sp017511465	79.2727	161	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062685.1	s__UBA9715 sp015062685	79.204	183	457	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:47:39,873] [INFO] GTDB search result was written to GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/result_gtdb.tsv
[2023-06-05 10:47:39,874] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:47:39,877] [INFO] DFAST_QC result json was written to GCA_902780685.1_Rumen_uncultured_genome_RUG12598_genomic.fna/dqc_result.json
[2023-06-05 10:47:39,877] [INFO] DFAST_QC completed!
[2023-06-05 10:47:39,877] [INFO] Total running time: 0h0m42s