[2023-06-08 10:20:02,005] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:20:02,007] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:20:02,007] [INFO] DQC Reference Directory: /var/lib/cwl/stga0df6f61-d0ff-4b5c-a064-1d8ada25a29c/dqc_reference
[2023-06-08 10:20:03,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:20:03,858] [INFO] Task started: Prodigal
[2023-06-08 10:20:03,858] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c5fc030-accd-4681-a921-60a47b1e9efd/GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna.gz | prodigal -d GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/cds.fna -a GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:20:15,364] [INFO] Task succeeded: Prodigal
[2023-06-08 10:20:15,365] [INFO] Task started: HMMsearch
[2023-06-08 10:20:15,365] [INFO] Running command: hmmsearch --tblout GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0df6f61-d0ff-4b5c-a064-1d8ada25a29c/dqc_reference/reference_markers.hmm GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:20:15,611] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:20:15,613] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1c5fc030-accd-4681-a921-60a47b1e9efd/GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna.gz]
[2023-06-08 10:20:15,637] [INFO] Query marker FASTA was written to GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/markers.fasta
[2023-06-08 10:20:15,638] [INFO] Task started: Blastn
[2023-06-08 10:20:15,638] [INFO] Running command: blastn -query GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/markers.fasta -db /var/lib/cwl/stga0df6f61-d0ff-4b5c-a064-1d8ada25a29c/dqc_reference/reference_markers.fasta -out GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:20:16,285] [INFO] Task succeeded: Blastn
[2023-06-08 10:20:16,290] [INFO] Selected 21 target genomes.
[2023-06-08 10:20:16,290] [INFO] Target genome list was writen to GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/target_genomes.txt
[2023-06-08 10:20:16,295] [INFO] Task started: fastANI
[2023-06-08 10:20:16,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c5fc030-accd-4681-a921-60a47b1e9efd/GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna.gz --refList GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/target_genomes.txt --output GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:20:30,527] [INFO] Task succeeded: fastANI
[2023-06-08 10:20:30,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0df6f61-d0ff-4b5c-a064-1d8ada25a29c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:20:30,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0df6f61-d0ff-4b5c-a064-1d8ada25a29c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:20:30,530] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:20:30,530] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 10:20:30,531] [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
--------------------------------------------------------------------------------
[2023-06-08 10:20:30,532] [INFO] DFAST Taxonomy check result was written to GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/tc_result.tsv
[2023-06-08 10:20:30,533] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:20:30,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:20:30,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0df6f61-d0ff-4b5c-a064-1d8ada25a29c/dqc_reference/checkm_data
[2023-06-08 10:20:30,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:20:30,564] [INFO] Task started: CheckM
[2023-06-08 10:20:30,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/checkm_input GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/checkm_result
[2023-06-08 10:21:06,784] [INFO] Task succeeded: CheckM
[2023-06-08 10:21:06,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:21:06,805] [INFO] ===== Completeness check finished =====
[2023-06-08 10:21:06,806] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:21:06,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/markers.fasta)
[2023-06-08 10:21:06,806] [INFO] Task started: Blastn
[2023-06-08 10:21:06,806] [INFO] Running command: blastn -query GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/markers.fasta -db /var/lib/cwl/stga0df6f61-d0ff-4b5c-a064-1d8ada25a29c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:21:07,809] [INFO] Task succeeded: Blastn
[2023-06-08 10:21:07,814] [INFO] Selected 13 target genomes.
[2023-06-08 10:21:07,814] [INFO] Target genome list was writen to GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:21:07,843] [INFO] Task started: fastANI
[2023-06-08 10:21:07,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c5fc030-accd-4681-a921-60a47b1e9efd/GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna.gz --refList GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/target_genomes_gtdb.txt --output GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:21:12,949] [INFO] Task succeeded: fastANI
[2023-06-08 10:21:12,961] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:21:12,961] [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_002394335.1	s__RF16 sp002394335	97.4671	569	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.97	97.59	0.88	0.85	8	conclusive
GCA_905233255.1	s__RF16 sp905233255	80.0057	218	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779705.1	s__RF16 sp902779705	79.3745	240	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	98.39	98.39	0.92	0.92	2	-
GCA_017448345.1	s__RF16 sp017448345	79.0176	184	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.94	97.15	0.82	0.75	3	-
GCA_002354055.1	s__RF16 sp002354055	78.8496	170	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	95.95	95.67	0.83	0.82	3	-
GCA_002392745.1	s__RF16 sp002392745	78.6693	153	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.66	96.65	0.84	0.83	3	-
GCA_017509715.1	s__RF16 sp017509715	78.5812	190	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319645.1	s__RF16 sp900319645	78.5133	177	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.68	95.36	0.92	0.85	3	-
GCA_002371785.1	s__RF16 sp002371785	78.2244	158	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.16	96.55	0.78	0.72	5	-
GCA_900318245.1	s__RF16 sp900318245	78.2214	150	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.37	96.49	0.89	0.84	5	-
GCA_017425065.1	s__RF16 sp017425065	78.1053	146	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017402895.1	s__RF16 sp017402895	77.2448	87	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387325.1	s__RF16 sp002387325	77.1442	73	657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	98.76	98.76	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-08 10:21:12,963] [INFO] GTDB search result was written to GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/result_gtdb.tsv
[2023-06-08 10:21:12,963] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:21:12,967] [INFO] DFAST_QC result json was written to GCA_902802425.1_Rumen_uncultured_genome_RUG14769_genomic.fna/dqc_result.json
[2023-06-08 10:21:12,967] [INFO] DFAST_QC completed!
[2023-06-08 10:21:12,967] [INFO] Total running time: 0h1m11s