[2023-06-29 16:53:32,110] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:53:32,120] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:53:32,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg73a324de-e045-4b6f-807a-09f1283035d5/dqc_reference
[2023-06-29 16:53:33,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:53:33,831] [INFO] Task started: Prodigal
[2023-06-29 16:53:33,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c1716f2-5ea7-4939-92c9-7577e76bf90d/GCA_021769725.1_ASM2176972v1_genomic.fna.gz | prodigal -d GCA_021769725.1_ASM2176972v1_genomic.fna/cds.fna -a GCA_021769725.1_ASM2176972v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:53:42,025] [INFO] Task succeeded: Prodigal
[2023-06-29 16:53:42,026] [INFO] Task started: HMMsearch
[2023-06-29 16:53:42,026] [INFO] Running command: hmmsearch --tblout GCA_021769725.1_ASM2176972v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73a324de-e045-4b6f-807a-09f1283035d5/dqc_reference/reference_markers.hmm GCA_021769725.1_ASM2176972v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:53:42,308] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:53:42,310] [INFO] Found 6/6 markers.
[2023-06-29 16:53:42,347] [INFO] Query marker FASTA was written to GCA_021769725.1_ASM2176972v1_genomic.fna/markers.fasta
[2023-06-29 16:53:42,348] [INFO] Task started: Blastn
[2023-06-29 16:53:42,348] [INFO] Running command: blastn -query GCA_021769725.1_ASM2176972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73a324de-e045-4b6f-807a-09f1283035d5/dqc_reference/reference_markers.fasta -out GCA_021769725.1_ASM2176972v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:53:42,973] [INFO] Task succeeded: Blastn
[2023-06-29 16:53:42,976] [INFO] Selected 14 target genomes.
[2023-06-29 16:53:42,977] [INFO] Target genome list was writen to GCA_021769725.1_ASM2176972v1_genomic.fna/target_genomes.txt
[2023-06-29 16:53:42,978] [INFO] Task started: fastANI
[2023-06-29 16:53:42,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c1716f2-5ea7-4939-92c9-7577e76bf90d/GCA_021769725.1_ASM2176972v1_genomic.fna.gz --refList GCA_021769725.1_ASM2176972v1_genomic.fna/target_genomes.txt --output GCA_021769725.1_ASM2176972v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:53:50,465] [INFO] Task succeeded: fastANI
[2023-06-29 16:53:50,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73a324de-e045-4b6f-807a-09f1283035d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:53:50,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73a324de-e045-4b6f-807a-09f1283035d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:53:50,474] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:53:50,474] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:53:50,475] [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
Ruminococcus flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	77.9008	171	1167	95	below_threshold
Ruminococcus bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	77.257	72	1167	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:53:50,477] [INFO] DFAST Taxonomy check result was written to GCA_021769725.1_ASM2176972v1_genomic.fna/tc_result.tsv
[2023-06-29 16:53:50,478] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:53:50,478] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:53:50,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73a324de-e045-4b6f-807a-09f1283035d5/dqc_reference/checkm_data
[2023-06-29 16:53:50,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:53:50,522] [INFO] Task started: CheckM
[2023-06-29 16:53:50,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021769725.1_ASM2176972v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021769725.1_ASM2176972v1_genomic.fna/checkm_input GCA_021769725.1_ASM2176972v1_genomic.fna/checkm_result
[2023-06-29 16:54:20,705] [INFO] Task succeeded: CheckM
[2023-06-29 16:54:20,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:54:20,730] [INFO] ===== Completeness check finished =====
[2023-06-29 16:54:20,730] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:54:20,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021769725.1_ASM2176972v1_genomic.fna/markers.fasta)
[2023-06-29 16:54:20,731] [INFO] Task started: Blastn
[2023-06-29 16:54:20,731] [INFO] Running command: blastn -query GCA_021769725.1_ASM2176972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73a324de-e045-4b6f-807a-09f1283035d5/dqc_reference/reference_markers_gtdb.fasta -out GCA_021769725.1_ASM2176972v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:54:21,786] [INFO] Task succeeded: Blastn
[2023-06-29 16:54:21,790] [INFO] Selected 14 target genomes.
[2023-06-29 16:54:21,790] [INFO] Target genome list was writen to GCA_021769725.1_ASM2176972v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:54:21,826] [INFO] Task started: fastANI
[2023-06-29 16:54:21,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c1716f2-5ea7-4939-92c9-7577e76bf90d/GCA_021769725.1_ASM2176972v1_genomic.fna.gz --refList GCA_021769725.1_ASM2176972v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021769725.1_ASM2176972v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:54:28,218] [INFO] Task succeeded: fastANI
[2023-06-29 16:54:28,233] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:54:28,233] [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_900545125.1	s__Ruminococcus sp900545125	91.1507	525	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	99.79	99.79	0.77	0.77	2	-
GCA_910579835.1	s__Ruminococcus sp910579835	80.2354	364	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461395.1	s__Ruminococcus sp017461395	80.2229	353	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017513795.1	s__Ruminococcus sp017513795	80.0381	365	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.92	97.92	0.90	0.90	2	-
GCA_017516465.1	s__Ruminococcus sp017516465	79.6334	340	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761275.1	s__Ruminococcus sp900761275	79.4574	290	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462565.1	s__Ruminococcus sp017462565	78.8166	331	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556875.1	s__Ruminococcus flavefaciens_S	77.8783	113	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577575.1	s__Ruminococcus sp910577575	77.8536	153	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016303195.1	s__Ruminococcus sp016303195	77.4285	88	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362965.1	s__UBA1394 sp900066845	77.4142	90	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394	95.0	98.61	98.18	0.90	0.86	6	-
GCA_017479805.1	s__Ruminococcus sp017479805	77.3725	107	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418765.1	s__Ruminococcus sp017418765	77.1456	83	1167	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:54:28,235] [INFO] GTDB search result was written to GCA_021769725.1_ASM2176972v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:54:28,236] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:54:28,239] [INFO] DFAST_QC result json was written to GCA_021769725.1_ASM2176972v1_genomic.fna/dqc_result.json
[2023-06-29 16:54:28,239] [INFO] DFAST_QC completed!
[2023-06-29 16:54:28,239] [INFO] Total running time: 0h0m56s