[2023-06-05 01:30:58,704] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:30:58,707] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:30:58,707] [INFO] DQC Reference Directory: /var/lib/cwl/stge49e055d-9823-4ce6-b6b9-fcd6a2752880/dqc_reference
[2023-06-05 01:31:00,058] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:31:00,059] [INFO] Task started: Prodigal
[2023-06-05 01:31:00,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ed8fb00-4fc8-4fac-97d0-19a12be85b02/GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna.gz | prodigal -d GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/cds.fna -a GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:31:06,647] [INFO] Task succeeded: Prodigal
[2023-06-05 01:31:06,648] [INFO] Task started: HMMsearch
[2023-06-05 01:31:06,648] [INFO] Running command: hmmsearch --tblout GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge49e055d-9823-4ce6-b6b9-fcd6a2752880/dqc_reference/reference_markers.hmm GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:31:06,966] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:31:06,968] [INFO] Found 6/6 markers.
[2023-06-05 01:31:07,015] [INFO] Query marker FASTA was written to GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/markers.fasta
[2023-06-05 01:31:07,015] [INFO] Task started: Blastn
[2023-06-05 01:31:07,015] [INFO] Running command: blastn -query GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/markers.fasta -db /var/lib/cwl/stge49e055d-9823-4ce6-b6b9-fcd6a2752880/dqc_reference/reference_markers.fasta -out GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:31:07,655] [INFO] Task succeeded: Blastn
[2023-06-05 01:31:07,659] [INFO] Selected 29 target genomes.
[2023-06-05 01:31:07,660] [INFO] Target genome list was writen to GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/target_genomes.txt
[2023-06-05 01:31:07,669] [INFO] Task started: fastANI
[2023-06-05 01:31:07,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ed8fb00-4fc8-4fac-97d0-19a12be85b02/GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna.gz --refList GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/target_genomes.txt --output GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:31:23,769] [INFO] Task succeeded: fastANI
[2023-06-05 01:31:23,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge49e055d-9823-4ce6-b6b9-fcd6a2752880/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:31:23,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge49e055d-9823-4ce6-b6b9-fcd6a2752880/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:31:23,775] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:31:23,775] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:31:23,776] [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
Succiniclasticum ruminis	strain=DSM 9236	GCA_900112895.1	40841	40841	suspected-type	True	86.7771	534	784	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:31:23,778] [INFO] DFAST Taxonomy check result was written to GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/tc_result.tsv
[2023-06-05 01:31:23,779] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:31:23,779] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:31:23,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge49e055d-9823-4ce6-b6b9-fcd6a2752880/dqc_reference/checkm_data
[2023-06-05 01:31:23,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:31:23,808] [INFO] Task started: CheckM
[2023-06-05 01:31:23,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/checkm_input GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/checkm_result
[2023-06-05 01:31:49,267] [INFO] Task succeeded: CheckM
[2023-06-05 01:31:49,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:31:49,289] [INFO] ===== Completeness check finished =====
[2023-06-05 01:31:49,289] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:31:49,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/markers.fasta)
[2023-06-05 01:31:49,290] [INFO] Task started: Blastn
[2023-06-05 01:31:49,290] [INFO] Running command: blastn -query GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/markers.fasta -db /var/lib/cwl/stge49e055d-9823-4ce6-b6b9-fcd6a2752880/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:31:50,066] [INFO] Task succeeded: Blastn
[2023-06-05 01:31:50,071] [INFO] Selected 20 target genomes.
[2023-06-05 01:31:50,072] [INFO] Target genome list was writen to GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:31:50,086] [INFO] Task started: fastANI
[2023-06-05 01:31:50,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ed8fb00-4fc8-4fac-97d0-19a12be85b02/GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna.gz --refList GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/target_genomes_gtdb.txt --output GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:31:59,668] [INFO] Task succeeded: fastANI
[2023-06-05 01:31:59,683] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:31:59,683] [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_900315925.1	s__Succiniclasticum sp900315925	95.8394	598	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	96.41	95.14	0.84	0.70	42	conclusive
GCF_900112895.1	s__Succiniclasticum ruminis	86.7774	534	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405945.1	s__Succiniclasticum sp017405945	86.5202	495	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801365.1	s__Succiniclasticum sp902801365	86.3123	468	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.72	97.62	0.82	0.80	3	-
GCA_017443165.1	s__Succiniclasticum sp017443165	84.6426	262	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233365.1	s__Succiniclasticum sp905233365	84.3997	466	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	98.76	98.76	0.84	0.84	2	-
GCA_003512125.1	s__Succiniclasticum sp003512125	83.1108	306	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	98.84	98.84	0.85	0.85	2	-
GCA_017554485.1	s__Succiniclasticum sp017554485	81.9698	436	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342505.1	s__Succiniclasticum sp002342505	81.0916	301	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.62	97.51	0.81	0.72	6	-
GCA_900315345.1	s__Succiniclasticum sp900315345	81.0502	398	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.51	96.16	0.86	0.76	12	-
GCA_017460905.1	s__Succiniclasticum sp017460905	80.7395	300	784	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum	95.0	97.67	97.67	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-06-05 01:31:59,685] [INFO] GTDB search result was written to GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/result_gtdb.tsv
[2023-06-05 01:31:59,685] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:31:59,688] [INFO] DFAST_QC result json was written to GCA_902782005.1_Rumen_uncultured_genome_RUG12727_genomic.fna/dqc_result.json
[2023-06-05 01:31:59,689] [INFO] DFAST_QC completed!
[2023-06-05 01:31:59,689] [INFO] Total running time: 0h1m1s