[2023-06-05 18:56:51,928] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:56:51,932] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:56:51,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg65726c43-9d3b-42d1-958a-c012dda86d58/dqc_reference
[2023-06-05 18:56:53,871] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:56:53,872] [INFO] Task started: Prodigal
[2023-06-05 18:56:53,872] [INFO] Running command: gunzip -c /var/lib/cwl/stgb76b722c-9e01-4123-9071-7aff76d4d502/GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna.gz | prodigal -d GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/cds.fna -a GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:29,560] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:29,561] [INFO] Task started: HMMsearch
[2023-06-05 18:57:29,561] [INFO] Running command: hmmsearch --tblout GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65726c43-9d3b-42d1-958a-c012dda86d58/dqc_reference/reference_markers.hmm GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:29,837] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:29,838] [INFO] Found 6/6 markers.
[2023-06-05 18:57:29,873] [INFO] Query marker FASTA was written to GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/markers.fasta
[2023-06-05 18:57:29,873] [INFO] Task started: Blastn
[2023-06-05 18:57:29,873] [INFO] Running command: blastn -query GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/markers.fasta -db /var/lib/cwl/stg65726c43-9d3b-42d1-958a-c012dda86d58/dqc_reference/reference_markers.fasta -out GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:30,466] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:30,470] [INFO] Selected 19 target genomes.
[2023-06-05 18:57:30,471] [INFO] Target genome list was writen to GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/target_genomes.txt
[2023-06-05 18:57:30,478] [INFO] Task started: fastANI
[2023-06-05 18:57:30,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgb76b722c-9e01-4123-9071-7aff76d4d502/GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna.gz --refList GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/target_genomes.txt --output GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:57:42,338] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:42,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65726c43-9d3b-42d1-958a-c012dda86d58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:57:42,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65726c43-9d3b-42d1-958a-c012dda86d58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:57:42,344] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:57:42,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:57:42,344] [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
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	78.2665	250	1185	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	78.1321	243	1185	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.5437	56	1185	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:57:42,347] [INFO] DFAST Taxonomy check result was written to GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/tc_result.tsv
[2023-06-05 18:57:42,348] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:57:42,348] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:57:42,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65726c43-9d3b-42d1-958a-c012dda86d58/dqc_reference/checkm_data
[2023-06-05 18:57:42,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:57:42,398] [INFO] Task started: CheckM
[2023-06-05 18:57:42,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/checkm_input GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/checkm_result
[2023-06-05 18:58:52,418] [INFO] Task succeeded: CheckM
[2023-06-05 18:58:52,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:58:52,440] [INFO] ===== Completeness check finished =====
[2023-06-05 18:58:52,440] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:58:52,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/markers.fasta)
[2023-06-05 18:58:52,441] [INFO] Task started: Blastn
[2023-06-05 18:58:52,441] [INFO] Running command: blastn -query GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/markers.fasta -db /var/lib/cwl/stg65726c43-9d3b-42d1-958a-c012dda86d58/dqc_reference/reference_markers_gtdb.fasta -out GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:53,431] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:53,436] [INFO] Selected 10 target genomes.
[2023-06-05 18:58:53,436] [INFO] Target genome list was writen to GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:58:53,440] [INFO] Task started: fastANI
[2023-06-05 18:58:53,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgb76b722c-9e01-4123-9071-7aff76d4d502/GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna.gz --refList GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/target_genomes_gtdb.txt --output GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:59:01,435] [INFO] Task succeeded: fastANI
[2023-06-05 18:59:01,450] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:59:01,450] [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_902781045.1	s__Sodaliphilus sp902781045	100.0	1175	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.92	97.92	0.86	0.86	2	conclusive
GCA_017477555.1	s__Sodaliphilus sp017477555	85.9781	696	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.74	97.72	0.83	0.78	3	-
GCA_002353885.1	s__Sodaliphilus sp002353885	85.7134	705	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.50	97.13	0.86	0.82	5	-
GCA_002396085.1	s__Sodaliphilus sp002396085	84.9514	660	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.76	97.72	0.87	0.86	3	-
GCA_016290765.1	s__Sodaliphilus sp016290765	80.5958	487	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557285.1	s__Sodaliphilus sp017557285	80.4012	350	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016281825.1	s__Sodaliphilus sp016281825	80.2938	469	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776835.1	s__Sodaliphilus sp902776835	79.1062	371	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.85	97.41	0.91	0.88	8	-
GCA_900318865.1	s__Sodaliphilus sp900318865	78.7423	297	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.72	97.82	0.92	0.87	5	-
GCA_902792895.1	s__Sodaliphilus sp902792895	78.3899	322	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:59:01,452] [INFO] GTDB search result was written to GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/result_gtdb.tsv
[2023-06-05 18:59:01,453] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:59:01,456] [INFO] DFAST_QC result json was written to GCA_902781045.1_Rumen_uncultured_genome_RUG12632_genomic.fna/dqc_result.json
[2023-06-05 18:59:01,456] [INFO] DFAST_QC completed!
[2023-06-05 18:59:01,457] [INFO] Total running time: 0h2m10s