[2023-06-07 21:33:18,424] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:33:18,431] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:33:18,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg7900624e-8f98-4280-9b8b-251ad6d685af/dqc_reference
[2023-06-07 21:33:20,092] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:33:20,093] [INFO] Task started: Prodigal
[2023-06-07 21:33:20,093] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b055db4-327b-4190-abdd-eae48ab17348/GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna.gz | prodigal -d GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/cds.fna -a GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:33:25,683] [INFO] Task succeeded: Prodigal
[2023-06-07 21:33:25,683] [INFO] Task started: HMMsearch
[2023-06-07 21:33:25,683] [INFO] Running command: hmmsearch --tblout GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7900624e-8f98-4280-9b8b-251ad6d685af/dqc_reference/reference_markers.hmm GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:33:25,970] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:33:25,972] [INFO] Found 6/6 markers.
[2023-06-07 21:33:26,005] [INFO] Query marker FASTA was written to GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/markers.fasta
[2023-06-07 21:33:26,006] [INFO] Task started: Blastn
[2023-06-07 21:33:26,006] [INFO] Running command: blastn -query GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/markers.fasta -db /var/lib/cwl/stg7900624e-8f98-4280-9b8b-251ad6d685af/dqc_reference/reference_markers.fasta -out GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:33:26,592] [INFO] Task succeeded: Blastn
[2023-06-07 21:33:26,596] [INFO] Selected 23 target genomes.
[2023-06-07 21:33:26,596] [INFO] Target genome list was writen to GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/target_genomes.txt
[2023-06-07 21:33:26,599] [INFO] Task started: fastANI
[2023-06-07 21:33:26,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b055db4-327b-4190-abdd-eae48ab17348/GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna.gz --refList GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/target_genomes.txt --output GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:33:39,794] [INFO] Task succeeded: fastANI
[2023-06-07 21:33:39,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7900624e-8f98-4280-9b8b-251ad6d685af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:33:39,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7900624e-8f98-4280-9b8b-251ad6d685af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:33:39,801] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:33:39,801] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:33:39,802] [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
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	78.2961	119	842	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	77.528	59	842	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	77.3816	59	842	95	below_threshold
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	76.9581	54	842	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:33:39,804] [INFO] DFAST Taxonomy check result was written to GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/tc_result.tsv
[2023-06-07 21:33:39,804] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:33:39,805] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:33:39,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7900624e-8f98-4280-9b8b-251ad6d685af/dqc_reference/checkm_data
[2023-06-07 21:33:39,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:33:39,841] [INFO] Task started: CheckM
[2023-06-07 21:33:39,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/checkm_input GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/checkm_result
[2023-06-07 21:34:03,398] [INFO] Task succeeded: CheckM
[2023-06-07 21:34:03,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:34:03,421] [INFO] ===== Completeness check finished =====
[2023-06-07 21:34:03,421] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:34:03,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/markers.fasta)
[2023-06-07 21:34:03,422] [INFO] Task started: Blastn
[2023-06-07 21:34:03,422] [INFO] Running command: blastn -query GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/markers.fasta -db /var/lib/cwl/stg7900624e-8f98-4280-9b8b-251ad6d685af/dqc_reference/reference_markers_gtdb.fasta -out GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:34:04,204] [INFO] Task succeeded: Blastn
[2023-06-07 21:34:04,208] [INFO] Selected 16 target genomes.
[2023-06-07 21:34:04,209] [INFO] Target genome list was writen to GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:34:04,217] [INFO] Task started: fastANI
[2023-06-07 21:34:04,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b055db4-327b-4190-abdd-eae48ab17348/GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna.gz --refList GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/target_genomes_gtdb.txt --output GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:34:11,910] [INFO] Task succeeded: fastANI
[2023-06-07 21:34:11,925] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:34:11,926] [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_900316715.1	s__Eubacterium_Q sp900316715	100.0	830	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.73	96.50	0.86	0.78	14	conclusive
GCA_002350525.1	s__Eubacterium_Q sp002350525	84.7574	611	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.75	97.74	0.91	0.85	4	-
GCA_902780985.1	s__Eubacterium_Q sp902780985	84.0545	431	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017634555.1	s__Eubacterium_Q sp017634555	81.0207	302	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017519155.1	s__Eubacterium_Q sp017519155	79.2042	140	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000687975.1	s__Eubacterium_Q sp000687975	78.9876	216	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774725.1	s__Eubacterium_Q sp902774725	78.6891	123	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	96.31	95.93	0.76	0.75	3	-
GCA_900199595.1	s__Eubacterium_Q sp900199595	78.6622	176	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760415.1	s__Eubacterium_Q sp002349225	78.4668	163	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.66	98.14	0.88	0.86	4	-
GCA_017430325.1	s__Eubacterium_Q sp017430325	78.3446	120	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.28	98.28	0.91	0.91	2	-
GCF_900167085.1	s__Eubacterium_Q ruminantium	78.2961	119	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	99.19	98.63	0.97	0.94	6	-
GCA_002392655.1	s__Eubacterium_Q sp002392655	78.1242	136	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520205.1	s__Eubacterium_Q sp003520205	77.5089	89	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	97.98	97.98	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-07 21:34:11,928] [INFO] GTDB search result was written to GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/result_gtdb.tsv
[2023-06-07 21:34:11,928] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:34:11,931] [INFO] DFAST_QC result json was written to GCA_902757355.1_Rumen_uncultured_genome_RUG10254_genomic.fna/dqc_result.json
[2023-06-07 21:34:11,932] [INFO] DFAST_QC completed!
[2023-06-07 21:34:11,932] [INFO] Total running time: 0h0m54s