[2023-06-08 10:40:34,020] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:40:34,022] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:40:34,022] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8851f87-04a6-4d0e-9022-ec035e08b60c/dqc_reference
[2023-06-08 10:40:35,201] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:40:35,201] [INFO] Task started: Prodigal
[2023-06-08 10:40:35,202] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fba7ad9-aa41-4a9a-99c1-c6af2b283a04/GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna.gz | prodigal -d GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/cds.fna -a GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:40:39,329] [INFO] Task succeeded: Prodigal
[2023-06-08 10:40:39,329] [INFO] Task started: HMMsearch
[2023-06-08 10:40:39,329] [INFO] Running command: hmmsearch --tblout GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8851f87-04a6-4d0e-9022-ec035e08b60c/dqc_reference/reference_markers.hmm GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:40:39,551] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:40:39,553] [INFO] Found 6/6 markers.
[2023-06-08 10:40:39,594] [INFO] Query marker FASTA was written to GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/markers.fasta
[2023-06-08 10:40:39,594] [INFO] Task started: Blastn
[2023-06-08 10:40:39,594] [INFO] Running command: blastn -query GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8851f87-04a6-4d0e-9022-ec035e08b60c/dqc_reference/reference_markers.fasta -out GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:40:40,249] [INFO] Task succeeded: Blastn
[2023-06-08 10:40:40,253] [INFO] Selected 19 target genomes.
[2023-06-08 10:40:40,254] [INFO] Target genome list was writen to GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/target_genomes.txt
[2023-06-08 10:40:40,257] [INFO] Task started: fastANI
[2023-06-08 10:40:40,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fba7ad9-aa41-4a9a-99c1-c6af2b283a04/GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna.gz --refList GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/target_genomes.txt --output GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:40:48,355] [INFO] Task succeeded: fastANI
[2023-06-08 10:40:48,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8851f87-04a6-4d0e-9022-ec035e08b60c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:40:48,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8851f87-04a6-4d0e-9022-ec035e08b60c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:40:48,367] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:40:48,367] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 10:40:48,368] [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
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.096	53	551	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.8708	53	551	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.7931	70	551	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.7489	67	551	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.6553	67	551	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 10:40:48,370] [INFO] DFAST Taxonomy check result was written to GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/tc_result.tsv
[2023-06-08 10:40:48,371] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:40:48,371] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:40:48,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8851f87-04a6-4d0e-9022-ec035e08b60c/dqc_reference/checkm_data
[2023-06-08 10:40:48,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:40:48,399] [INFO] Task started: CheckM
[2023-06-08 10:40:48,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/checkm_input GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/checkm_result
[2023-06-08 10:41:07,304] [INFO] Task succeeded: CheckM
[2023-06-08 10:41:07,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:41:07,326] [INFO] ===== Completeness check finished =====
[2023-06-08 10:41:07,326] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:41:07,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/markers.fasta)
[2023-06-08 10:41:07,327] [INFO] Task started: Blastn
[2023-06-08 10:41:07,327] [INFO] Running command: blastn -query GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8851f87-04a6-4d0e-9022-ec035e08b60c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:41:08,409] [INFO] Task succeeded: Blastn
[2023-06-08 10:41:08,414] [INFO] Selected 10 target genomes.
[2023-06-08 10:41:08,414] [INFO] Target genome list was writen to GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:41:08,420] [INFO] Task started: fastANI
[2023-06-08 10:41:08,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fba7ad9-aa41-4a9a-99c1-c6af2b283a04/GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna.gz --refList GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/target_genomes_gtdb.txt --output GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:41:12,858] [INFO] Task succeeded: fastANI
[2023-06-08 10:41:12,872] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:41:12,872] [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_900319935.1	s__Limivicinus sp900319935	98.844	461	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.02	98.62	0.86	0.80	6	conclusive
GCA_017403885.1	s__Limivicinus sp017403885	88.4752	396	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447645.1	s__Limivicinus sp017447645	88.0911	390	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449185.1	s__Limivicinus sp017449185	86.1231	363	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761055.1	s__Limivicinus sp902761055	86.1168	421	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450075.1	s__Limivicinus sp002450075	84.0859	331	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.03	97.77	0.79	0.75	6	-
GCA_900320595.1	s__Limivicinus sp900320595	83.6909	384	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.20	98.25	0.89	0.82	4	-
GCA_017444665.1	s__Limivicinus sp017444665	82.7264	304	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319835.1	s__Limivicinus sp900319835	79.9611	216	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017411225.1	s__CAG-103 sp017411225	78.3123	134	551	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 10:41:12,874] [INFO] GTDB search result was written to GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/result_gtdb.tsv
[2023-06-08 10:41:12,874] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:41:12,877] [INFO] DFAST_QC result json was written to GCA_902778795.1_Rumen_uncultured_genome_RUG12407_genomic.fna/dqc_result.json
[2023-06-08 10:41:12,877] [INFO] DFAST_QC completed!
[2023-06-08 10:41:12,877] [INFO] Total running time: 0h0m39s