[2023-06-08 03:14:11,414] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:14:11,417] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:14:11,418] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2882c69-b3a9-489c-b0d7-e4fbe7bc2271/dqc_reference
[2023-06-08 03:14:13,176] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:14:13,177] [INFO] Task started: Prodigal
[2023-06-08 03:14:13,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg36f3d9dd-671a-4c79-8d16-db6b4276d3f3/GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna.gz | prodigal -d GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/cds.fna -a GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:14:30,441] [INFO] Task succeeded: Prodigal
[2023-06-08 03:14:30,442] [INFO] Task started: HMMsearch
[2023-06-08 03:14:30,442] [INFO] Running command: hmmsearch --tblout GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2882c69-b3a9-489c-b0d7-e4fbe7bc2271/dqc_reference/reference_markers.hmm GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:14:30,703] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:14:30,704] [INFO] Found 6/6 markers.
[2023-06-08 03:14:30,760] [INFO] Query marker FASTA was written to GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/markers.fasta
[2023-06-08 03:14:30,760] [INFO] Task started: Blastn
[2023-06-08 03:14:30,761] [INFO] Running command: blastn -query GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2882c69-b3a9-489c-b0d7-e4fbe7bc2271/dqc_reference/reference_markers.fasta -out GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:31,387] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:31,390] [INFO] Selected 28 target genomes.
[2023-06-08 03:14:31,390] [INFO] Target genome list was writen to GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/target_genomes.txt
[2023-06-08 03:14:31,395] [INFO] Task started: fastANI
[2023-06-08 03:14:31,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg36f3d9dd-671a-4c79-8d16-db6b4276d3f3/GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna.gz --refList GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/target_genomes.txt --output GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:14:49,762] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:49,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2882c69-b3a9-489c-b0d7-e4fbe7bc2271/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:14:49,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2882c69-b3a9-489c-b0d7-e4fbe7bc2271/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:14:49,780] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:14:49,781] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 03:14:49,781] [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
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.4674	67	957	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	76.4674	67	957	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	76.4168	65	957	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.3543	58	957	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.274	58	957	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.2119	51	957	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	76.202	55	957	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	74.9118	52	957	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 03:14:49,783] [INFO] DFAST Taxonomy check result was written to GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/tc_result.tsv
[2023-06-08 03:14:49,784] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:14:49,784] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:14:49,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2882c69-b3a9-489c-b0d7-e4fbe7bc2271/dqc_reference/checkm_data
[2023-06-08 03:14:49,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:14:49,821] [INFO] Task started: CheckM
[2023-06-08 03:14:49,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/checkm_input GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/checkm_result
[2023-06-08 03:15:38,027] [INFO] Task succeeded: CheckM
[2023-06-08 03:15:38,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 3.70%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-08 03:15:38,051] [INFO] ===== Completeness check finished =====
[2023-06-08 03:15:38,052] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:15:38,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/markers.fasta)
[2023-06-08 03:15:38,052] [INFO] Task started: Blastn
[2023-06-08 03:15:38,052] [INFO] Running command: blastn -query GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2882c69-b3a9-489c-b0d7-e4fbe7bc2271/dqc_reference/reference_markers_gtdb.fasta -out GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:15:39,035] [INFO] Task succeeded: Blastn
[2023-06-08 03:15:39,040] [INFO] Selected 9 target genomes.
[2023-06-08 03:15:39,040] [INFO] Target genome list was writen to GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:15:39,041] [INFO] Task started: fastANI
[2023-06-08 03:15:39,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg36f3d9dd-671a-4c79-8d16-db6b4276d3f3/GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna.gz --refList GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/target_genomes_gtdb.txt --output GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:15:44,978] [INFO] Task succeeded: fastANI
[2023-06-08 03:15:44,994] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:15:44,994] [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_900318015.1	s__Cryptobacteroides sp900318015	97.704	835	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.28	97.03	0.89	0.81	4	conclusive
GCA_900316525.1	s__Cryptobacteroides sp900316525	91.7385	754	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.78	96.71	0.88	0.84	4	-
GCA_900316955.1	s__Cryptobacteroides sp900316955	91.4373	737	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017429205.1	s__Cryptobacteroides sp017429205	91.0375	611	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785065.1	s__Cryptobacteroides sp902785065	90.8712	684	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.77	97.77	0.84	0.84	2	-
GCA_017530725.1	s__Cryptobacteroides sp017530725	86.93	508	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017558775.1	s__Cryptobacteroides sp017558775	85.1518	594	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781705.1	s__Cryptobacteroides sp902781705	84.3027	597	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.56	96.56	0.81	0.81	2	-
GCA_017395045.1	s__Cryptobacteroides sp017395045	84.1539	534	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:15:44,996] [INFO] GTDB search result was written to GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/result_gtdb.tsv
[2023-06-08 03:15:44,996] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:15:44,999] [INFO] DFAST_QC result json was written to GCA_902787045.1_Rumen_uncultured_genome_RUG13228_genomic.fna/dqc_result.json
[2023-06-08 03:15:44,999] [INFO] DFAST_QC completed!
[2023-06-08 03:15:44,999] [INFO] Total running time: 0h1m34s