[2023-06-04 18:26:21,339] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:26:21,342] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:26:21,343] [INFO] DQC Reference Directory: /var/lib/cwl/stg8499d734-ebea-403b-933a-ab7d1bb52585/dqc_reference
[2023-06-04 18:26:22,920] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:26:22,922] [INFO] Task started: Prodigal
[2023-06-04 18:26:22,922] [INFO] Running command: gunzip -c /var/lib/cwl/stg74177914-6e7b-4884-b995-82d733a47c08/GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna.gz | prodigal -d GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/cds.fna -a GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:26:34,871] [INFO] Task succeeded: Prodigal
[2023-06-04 18:26:34,871] [INFO] Task started: HMMsearch
[2023-06-04 18:26:34,871] [INFO] Running command: hmmsearch --tblout GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8499d734-ebea-403b-933a-ab7d1bb52585/dqc_reference/reference_markers.hmm GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:26:35,134] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:26:35,137] [INFO] Found 6/6 markers.
[2023-06-04 18:26:35,166] [INFO] Query marker FASTA was written to GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/markers.fasta
[2023-06-04 18:26:35,166] [INFO] Task started: Blastn
[2023-06-04 18:26:35,166] [INFO] Running command: blastn -query GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/markers.fasta -db /var/lib/cwl/stg8499d734-ebea-403b-933a-ab7d1bb52585/dqc_reference/reference_markers.fasta -out GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:26:35,823] [INFO] Task succeeded: Blastn
[2023-06-04 18:26:35,827] [INFO] Selected 28 target genomes.
[2023-06-04 18:26:35,827] [INFO] Target genome list was writen to GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/target_genomes.txt
[2023-06-04 18:26:35,862] [INFO] Task started: fastANI
[2023-06-04 18:26:35,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg74177914-6e7b-4884-b995-82d733a47c08/GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna.gz --refList GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/target_genomes.txt --output GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:26:49,878] [INFO] Task succeeded: fastANI
[2023-06-04 18:26:49,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8499d734-ebea-403b-933a-ab7d1bb52585/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:26:49,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8499d734-ebea-403b-933a-ab7d1bb52585/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:26:49,880] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:26:49,880] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 18:26:49,880] [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
--------------------------------------------------------------------------------
[2023-06-04 18:26:49,883] [INFO] DFAST Taxonomy check result was written to GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/tc_result.tsv
[2023-06-04 18:26:49,884] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:26:49,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:26:49,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8499d734-ebea-403b-933a-ab7d1bb52585/dqc_reference/checkm_data
[2023-06-04 18:26:49,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:26:49,919] [INFO] Task started: CheckM
[2023-06-04 18:26:49,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/checkm_input GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/checkm_result
[2023-06-04 18:27:27,538] [INFO] Task succeeded: CheckM
[2023-06-04 18:27:27,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.22%
Contamintation: 15.51%
Strain heterogeneity: 37.50%
--------------------------------------------------------------------------------
[2023-06-04 18:27:27,564] [INFO] ===== Completeness check finished =====
[2023-06-04 18:27:27,564] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:27:27,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/markers.fasta)
[2023-06-04 18:27:27,565] [INFO] Task started: Blastn
[2023-06-04 18:27:27,565] [INFO] Running command: blastn -query GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/markers.fasta -db /var/lib/cwl/stg8499d734-ebea-403b-933a-ab7d1bb52585/dqc_reference/reference_markers_gtdb.fasta -out GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:27:28,457] [INFO] Task succeeded: Blastn
[2023-06-04 18:27:28,462] [INFO] Selected 19 target genomes.
[2023-06-04 18:27:28,462] [INFO] Target genome list was writen to GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:27:28,643] [INFO] Task started: fastANI
[2023-06-04 18:27:28,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg74177914-6e7b-4884-b995-82d733a47c08/GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna.gz --refList GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/target_genomes_gtdb.txt --output GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:27:35,989] [INFO] Task succeeded: fastANI
[2023-06-04 18:27:36,004] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:27:36,004] [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_900319685.1	s__Cryptobacteroides sp900319685	97.7556	435	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.13	0.85	0.68	20	conclusive
GCA_905235085.1	s__Cryptobacteroides sp905235085	86.5148	458	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017958985.1	s__Cryptobacteroides sp017958985	85.5772	382	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320185.1	s__Cryptobacteroides sp900320185	79.7496	191	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	98.37	0.88	0.82	11	-
GCA_017469745.1	s__Cryptobacteroides sp017469745	78.6161	206	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	78.5815	205	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_902780935.1	s__Cryptobacteroides sp902780935	78.464	181	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	97.52	0.84	0.84	2	-
GCA_902762655.1	s__Cryptobacteroides sp902762655	78.0277	70	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.32	98.07	0.81	0.76	4	-
GCA_000433355.1	s__Cryptobacteroides sp000433355	78.003	176	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	97.93	0.86	0.80	6	-
GCA_900544195.1	s__Cryptobacteroides sp900544195	77.9447	180	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.99	97.97	0.92	0.84	3	-
GCA_002314195.1	s__Cryptobacteroides sp002314195	77.7582	149	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.70	98.15	0.81	0.75	7	-
GCA_900313275.1	s__Cryptobacteroides sp900313275	77.517	113	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.24	97.20	0.92	0.82	4	-
GCA_017962025.1	s__Cryptobacteroides sp017962025	77.403	158	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797035.1	s__Cryptobacteroides sp902797035	77.3019	155	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066065.1	s__Cryptobacteroides sp018066065	77.1256	115	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016283985.1	s__Cryptobacteroides sp016283985	76.9407	62	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427385.1	s__Cryptobacteroides sp017427385	76.6573	61	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962925.1	s__Cryptobacteroides sp017962925	76.3903	55	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 18:27:36,008] [INFO] GTDB search result was written to GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/result_gtdb.tsv
[2023-06-04 18:27:36,008] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:27:36,011] [INFO] DFAST_QC result json was written to GCA_902792475.1_Rumen_uncultured_genome_RUG13782_genomic.fna/dqc_result.json
[2023-06-04 18:27:36,012] [INFO] DFAST_QC completed!
[2023-06-04 18:27:36,012] [INFO] Total running time: 0h1m15s