[2023-06-08 12:26:23,618] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:26:23,623] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:26:23,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e827043-642f-4a37-88c0-52f6782c1a22/dqc_reference
[2023-06-08 12:26:24,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:26:24,843] [INFO] Task started: Prodigal
[2023-06-08 12:26:24,843] [INFO] Running command: gunzip -c /var/lib/cwl/stge14f647e-f6d4-41fa-9768-d648e6433891/GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna.gz | prodigal -d GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/cds.fna -a GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:26:36,789] [INFO] Task succeeded: Prodigal
[2023-06-08 12:26:36,790] [INFO] Task started: HMMsearch
[2023-06-08 12:26:36,790] [INFO] Running command: hmmsearch --tblout GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e827043-642f-4a37-88c0-52f6782c1a22/dqc_reference/reference_markers.hmm GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:26:37,063] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:26:37,065] [INFO] Found 6/6 markers.
[2023-06-08 12:26:37,094] [INFO] Query marker FASTA was written to GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/markers.fasta
[2023-06-08 12:26:37,094] [INFO] Task started: Blastn
[2023-06-08 12:26:37,095] [INFO] Running command: blastn -query GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e827043-642f-4a37-88c0-52f6782c1a22/dqc_reference/reference_markers.fasta -out GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:26:37,670] [INFO] Task succeeded: Blastn
[2023-06-08 12:26:37,674] [INFO] Selected 19 target genomes.
[2023-06-08 12:26:37,674] [INFO] Target genome list was writen to GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/target_genomes.txt
[2023-06-08 12:26:37,677] [INFO] Task started: fastANI
[2023-06-08 12:26:37,677] [INFO] Running command: fastANI --query /var/lib/cwl/stge14f647e-f6d4-41fa-9768-d648e6433891/GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna.gz --refList GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/target_genomes.txt --output GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:26:49,657] [INFO] Task succeeded: fastANI
[2023-06-08 12:26:49,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e827043-642f-4a37-88c0-52f6782c1a22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:26:49,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e827043-642f-4a37-88c0-52f6782c1a22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:26:49,660] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:26:49,661] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:26:49,661] [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 12:26:49,663] [INFO] DFAST Taxonomy check result was written to GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/tc_result.tsv
[2023-06-08 12:26:49,664] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:26:49,664] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:26:49,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e827043-642f-4a37-88c0-52f6782c1a22/dqc_reference/checkm_data
[2023-06-08 12:26:49,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:26:49,698] [INFO] Task started: CheckM
[2023-06-08 12:26:49,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/checkm_input GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/checkm_result
[2023-06-08 12:27:27,097] [INFO] Task succeeded: CheckM
[2023-06-08 12:27:27,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:27:27,120] [INFO] ===== Completeness check finished =====
[2023-06-08 12:27:27,121] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:27:27,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/markers.fasta)
[2023-06-08 12:27:27,122] [INFO] Task started: Blastn
[2023-06-08 12:27:27,122] [INFO] Running command: blastn -query GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e827043-642f-4a37-88c0-52f6782c1a22/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:27,958] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:27,961] [INFO] Selected 23 target genomes.
[2023-06-08 12:27:27,962] [INFO] Target genome list was writen to GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:27:27,968] [INFO] Task started: fastANI
[2023-06-08 12:27:27,969] [INFO] Running command: fastANI --query /var/lib/cwl/stge14f647e-f6d4-41fa-9768-d648e6433891/GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna.gz --refList GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/target_genomes_gtdb.txt --output GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:27:37,152] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:37,166] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:27:37,167] [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_900316045.1	s__Cryptobacteroides sp900316045	99.1745	564	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.88	98.47	0.88	0.73	37	conclusive
GCA_002320605.1	s__Cryptobacteroides sp002320605	94.0152	529	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433355.1	s__Cryptobacteroides sp000433355	77.6759	96	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	97.93	0.86	0.80	6	-
GCA_004552965.1	s__Cryptobacteroides sp004552965	77.351	62	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.55	98.04	0.91	0.85	9	-
GCA_002439875.1	s__Cryptobacteroides sp002439875	77.3049	67	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544195.1	s__Cryptobacteroides sp900544195	77.2579	94	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.99	97.97	0.92	0.84	3	-
GCA_002438845.1	s__Cryptobacteroides sp002438845	77.217	87	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.65	99.58	0.89	0.89	3	-
GCA_902801885.1	s__Cryptobacteroides sp902801885	77.1962	65	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.96	97.31	0.90	0.87	8	-
GCA_905235085.1	s__Cryptobacteroides sp905235085	77.1771	63	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297815.1	s__Cryptobacteroides sp002297815	77.0508	71	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.51	97.81	0.90	0.86	6	-
GCA_017627955.1	s__Cryptobacteroides sp017627955	77.0277	55	642	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	76.9853	69	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_902801205.1	s__Cryptobacteroides sp902801205	76.7271	50	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.36	98.05	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-08 12:27:37,192] [INFO] GTDB search result was written to GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/result_gtdb.tsv
[2023-06-08 12:27:37,192] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:27:37,197] [INFO] DFAST_QC result json was written to GCA_902763065.1_Rumen_uncultured_genome_RUG10821_genomic.fna/dqc_result.json
[2023-06-08 12:27:37,197] [INFO] DFAST_QC completed!
[2023-06-08 12:27:37,198] [INFO] Total running time: 0h1m14s