[2023-06-05 07:09:37,798] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:09:37,824] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:09:37,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1a2f32d-97c0-4bdb-a443-515d4f2c3edc/dqc_reference
[2023-06-05 07:09:39,676] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:09:39,677] [INFO] Task started: Prodigal
[2023-06-05 07:09:39,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bf0f11a-dccb-42ab-a529-9dba9e18f698/GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna.gz | prodigal -d GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/cds.fna -a GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:09:44,926] [INFO] Task succeeded: Prodigal
[2023-06-05 07:09:44,926] [INFO] Task started: HMMsearch
[2023-06-05 07:09:44,926] [INFO] Running command: hmmsearch --tblout GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1a2f32d-97c0-4bdb-a443-515d4f2c3edc/dqc_reference/reference_markers.hmm GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:09:45,144] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:09:45,145] [INFO] Found 6/6 markers.
[2023-06-05 07:09:45,180] [INFO] Query marker FASTA was written to GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/markers.fasta
[2023-06-05 07:09:45,180] [INFO] Task started: Blastn
[2023-06-05 07:09:45,181] [INFO] Running command: blastn -query GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1a2f32d-97c0-4bdb-a443-515d4f2c3edc/dqc_reference/reference_markers.fasta -out GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:09:45,787] [INFO] Task succeeded: Blastn
[2023-06-05 07:09:45,792] [INFO] Selected 30 target genomes.
[2023-06-05 07:09:45,793] [INFO] Target genome list was writen to GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/target_genomes.txt
[2023-06-05 07:09:45,795] [INFO] Task started: fastANI
[2023-06-05 07:09:45,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf0f11a-dccb-42ab-a529-9dba9e18f698/GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna.gz --refList GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/target_genomes.txt --output GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:10:00,311] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:00,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1a2f32d-97c0-4bdb-a443-515d4f2c3edc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:10:00,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1a2f32d-97c0-4bdb-a443-515d4f2c3edc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:10:00,323] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:10:00,324] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:10:00,324] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.1257	56	652	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.0831	56	652	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.9824	59	652	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.9313	51	652	95	below_threshold
Sporobacter termitidis	strain=DSM 10068	GCA_900130065.1	44749	44749	type	True	75.63	54	652	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:10:00,327] [INFO] DFAST Taxonomy check result was written to GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/tc_result.tsv
[2023-06-05 07:10:00,327] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:10:00,327] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:10:00,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1a2f32d-97c0-4bdb-a443-515d4f2c3edc/dqc_reference/checkm_data
[2023-06-05 07:10:00,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:10:00,357] [INFO] Task started: CheckM
[2023-06-05 07:10:00,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/checkm_input GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/checkm_result
[2023-06-05 07:10:22,613] [INFO] Task succeeded: CheckM
[2023-06-05 07:10:22,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 6.94%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-05 07:10:22,634] [INFO] ===== Completeness check finished =====
[2023-06-05 07:10:22,635] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:10:22,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/markers.fasta)
[2023-06-05 07:10:22,635] [INFO] Task started: Blastn
[2023-06-05 07:10:22,636] [INFO] Running command: blastn -query GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1a2f32d-97c0-4bdb-a443-515d4f2c3edc/dqc_reference/reference_markers_gtdb.fasta -out GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:10:23,537] [INFO] Task succeeded: Blastn
[2023-06-05 07:10:23,542] [INFO] Selected 18 target genomes.
[2023-06-05 07:10:23,543] [INFO] Target genome list was writen to GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:10:23,544] [INFO] Task started: fastANI
[2023-06-05 07:10:23,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf0f11a-dccb-42ab-a529-9dba9e18f698/GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna.gz --refList GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/target_genomes_gtdb.txt --output GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:10:32,157] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:32,173] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:10:32,173] [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_900317375.1	s__Limivicinus sp900317375	98.3834	576	652	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.11	95.61	0.84	0.72	56	conclusive
GCA_017538965.1	s__Limivicinus sp017538965	82.7887	418	652	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_017458065.1	s__Limivicinus sp017458065	80.0853	285	652	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_017458335.1	s__Limivicinus sp017458335	79.8742	245	652	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_902798545.1	s__Limivicinus sp902798545	79.55	208	652	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_017627975.1	s__Limivicinus sp017627975	79.5395	210	652	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_900319465.1	s__Limivicinus sp900319465	79.3682	173	652	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.77	99.67	0.93	0.92	4	-
GCA_902775985.1	s__Limivicinus sp902775985	79.3219	180	652	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.70	98.45	0.76	0.73	5	-
GCA_902795045.1	s__Limivicinus sp902795045	78.962	179	652	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.71	97.45	0.84	0.77	4	-
GCA_900319635.1	s__Limivicinus sp900319635	78.9087	156	652	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.84	96.83	0.85	0.76	6	-
GCA_902775355.1	s__Limivicinus sp902775355	78.8162	173	652	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_017428565.1	s__Limivicinus sp017428565	78.7102	170	652	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_017395085.1	s__Limivicinus sp017395085	78.6847	161	652	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.30	96.83	0.71	0.71	3	-
GCA_902761635.1	s__Limivicinus sp902761635	78.4557	185	652	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_905234575.1	s__CAJOIG01 sp905234575	77.6748	73	652	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJOIG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:10:32,175] [INFO] GTDB search result was written to GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/result_gtdb.tsv
[2023-06-05 07:10:32,176] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:10:32,179] [INFO] DFAST_QC result json was written to GCA_902758045.1_Rumen_uncultured_genome_RUG10322_genomic.fna/dqc_result.json
[2023-06-05 07:10:32,179] [INFO] DFAST_QC completed!
[2023-06-05 07:10:32,179] [INFO] Total running time: 0h0m54s