[2023-06-04 22:02:39,208] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:02:39,213] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:02:39,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4c89958-2545-423f-bb2e-3cf1910f2dfc/dqc_reference
[2023-06-04 22:02:40,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:02:40,543] [INFO] Task started: Prodigal
[2023-06-04 22:02:40,543] [INFO] Running command: gunzip -c /var/lib/cwl/stgb51c3287-8bb2-4fec-92be-3abadd8903ef/GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna.gz | prodigal -d GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/cds.fna -a GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:02:53,313] [INFO] Task succeeded: Prodigal
[2023-06-04 22:02:53,314] [INFO] Task started: HMMsearch
[2023-06-04 22:02:53,314] [INFO] Running command: hmmsearch --tblout GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4c89958-2545-423f-bb2e-3cf1910f2dfc/dqc_reference/reference_markers.hmm GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:02:53,548] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:02:53,549] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb51c3287-8bb2-4fec-92be-3abadd8903ef/GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna.gz]
[2023-06-04 22:02:53,574] [INFO] Query marker FASTA was written to GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/markers.fasta
[2023-06-04 22:02:53,575] [INFO] Task started: Blastn
[2023-06-04 22:02:53,575] [INFO] Running command: blastn -query GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4c89958-2545-423f-bb2e-3cf1910f2dfc/dqc_reference/reference_markers.fasta -out GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:02:54,188] [INFO] Task succeeded: Blastn
[2023-06-04 22:02:54,192] [INFO] Selected 30 target genomes.
[2023-06-04 22:02:54,193] [INFO] Target genome list was writen to GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/target_genomes.txt
[2023-06-04 22:02:54,195] [INFO] Task started: fastANI
[2023-06-04 22:02:54,195] [INFO] Running command: fastANI --query /var/lib/cwl/stgb51c3287-8bb2-4fec-92be-3abadd8903ef/GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna.gz --refList GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/target_genomes.txt --output GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:03:12,174] [INFO] Task succeeded: fastANI
[2023-06-04 22:03:12,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4c89958-2545-423f-bb2e-3cf1910f2dfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:03:12,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4c89958-2545-423f-bb2e-3cf1910f2dfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:03:12,177] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:03:12,177] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 22:03:12,177] [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 22:03:12,179] [INFO] DFAST Taxonomy check result was written to GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/tc_result.tsv
[2023-06-04 22:03:12,179] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:03:12,179] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:03:12,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4c89958-2545-423f-bb2e-3cf1910f2dfc/dqc_reference/checkm_data
[2023-06-04 22:03:12,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:03:12,212] [INFO] Task started: CheckM
[2023-06-04 22:03:12,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/checkm_input GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/checkm_result
[2023-06-04 22:03:50,944] [INFO] Task succeeded: CheckM
[2023-06-04 22:03:50,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.36%
Contamintation: 9.38%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-04 22:03:50,969] [INFO] ===== Completeness check finished =====
[2023-06-04 22:03:50,969] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:03:50,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/markers.fasta)
[2023-06-04 22:03:50,970] [INFO] Task started: Blastn
[2023-06-04 22:03:50,970] [INFO] Running command: blastn -query GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4c89958-2545-423f-bb2e-3cf1910f2dfc/dqc_reference/reference_markers_gtdb.fasta -out GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:03:51,906] [INFO] Task succeeded: Blastn
[2023-06-04 22:03:51,911] [INFO] Selected 13 target genomes.
[2023-06-04 22:03:51,911] [INFO] Target genome list was writen to GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:03:51,913] [INFO] Task started: fastANI
[2023-06-04 22:03:51,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgb51c3287-8bb2-4fec-92be-3abadd8903ef/GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna.gz --refList GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/target_genomes_gtdb.txt --output GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:03:57,250] [INFO] Task succeeded: fastANI
[2023-06-04 22:03:57,264] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:03:57,264] [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_900317845.1	s__Cryptobacteroides sp900317845	98.1408	568	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.57	95.18	0.88	0.74	22	conclusive
GCA_002354005.1	s__Cryptobacteroides sp002354005	94.4328	429	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.47	96.01	0.76	0.69	14	-
GCA_002371115.1	s__Cryptobacteroides sp002371115	85.6596	369	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.48	0.78	0.75	4	-
GCA_902788095.1	s__Cryptobacteroides sp902788095	84.7644	390	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.63	97.63	0.79	0.79	2	-
GCA_902794005.1	s__Cryptobacteroides sp902794005	81.8257	300	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.50	98.20	0.83	0.80	3	-
GCA_902774155.1	s__Cryptobacteroides sp902774155	81.5764	334	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.49	96.60	0.84	0.80	4	-
GCA_017480345.1	s__Cryptobacteroides sp017480345	81.5251	298	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.06	98.06	0.83	0.83	2	-
GCA_017447815.1	s__Cryptobacteroides sp017447815	81.4019	328	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794615.1	s__Cryptobacteroides sp902794615	81.2516	263	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.63	96.28	0.79	0.72	4	-
GCA_900318445.1	s__Cryptobacteroides sp900318445	80.8558	303	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.95	95.41	0.86	0.76	6	-
GCA_900321655.1	s__Cryptobacteroides sp900321655	80.4605	279	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.46	96.30	0.88	0.86	12	-
GCA_900319405.1	s__Cryptobacteroides sp900319405	80.2842	280	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-04 22:03:57,266] [INFO] GTDB search result was written to GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/result_gtdb.tsv
[2023-06-04 22:03:57,267] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:03:57,270] [INFO] DFAST_QC result json was written to GCA_902759455.1_Rumen_uncultured_genome_RUG10473_genomic.fna/dqc_result.json
[2023-06-04 22:03:57,270] [INFO] DFAST_QC completed!
[2023-06-04 22:03:57,270] [INFO] Total running time: 0h1m18s