[2023-06-28 05:54:04,237] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:54:04,239] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:54:04,239] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5424929-67b5-4adf-a934-dd96087e11a6/dqc_reference
[2023-06-28 05:54:06,570] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:54:06,571] [INFO] Task started: Prodigal
[2023-06-28 05:54:06,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f6a2aa3-df8d-4b09-ab93-eb412e2d239d/GCA_017965425.1_ASM1796542v1_genomic.fna.gz | prodigal -d GCA_017965425.1_ASM1796542v1_genomic.fna/cds.fna -a GCA_017965425.1_ASM1796542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:54:29,945] [INFO] Task succeeded: Prodigal
[2023-06-28 05:54:29,946] [INFO] Task started: HMMsearch
[2023-06-28 05:54:29,946] [INFO] Running command: hmmsearch --tblout GCA_017965425.1_ASM1796542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5424929-67b5-4adf-a934-dd96087e11a6/dqc_reference/reference_markers.hmm GCA_017965425.1_ASM1796542v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:54:30,209] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:54:30,210] [INFO] Found 6/6 markers.
[2023-06-28 05:54:30,246] [INFO] Query marker FASTA was written to GCA_017965425.1_ASM1796542v1_genomic.fna/markers.fasta
[2023-06-28 05:54:30,246] [INFO] Task started: Blastn
[2023-06-28 05:54:30,246] [INFO] Running command: blastn -query GCA_017965425.1_ASM1796542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5424929-67b5-4adf-a934-dd96087e11a6/dqc_reference/reference_markers.fasta -out GCA_017965425.1_ASM1796542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:54:30,870] [INFO] Task succeeded: Blastn
[2023-06-28 05:54:30,875] [INFO] Selected 25 target genomes.
[2023-06-28 05:54:30,876] [INFO] Target genome list was writen to GCA_017965425.1_ASM1796542v1_genomic.fna/target_genomes.txt
[2023-06-28 05:54:30,878] [INFO] Task started: fastANI
[2023-06-28 05:54:30,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f6a2aa3-df8d-4b09-ab93-eb412e2d239d/GCA_017965425.1_ASM1796542v1_genomic.fna.gz --refList GCA_017965425.1_ASM1796542v1_genomic.fna/target_genomes.txt --output GCA_017965425.1_ASM1796542v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:54:44,208] [INFO] Task succeeded: fastANI
[2023-06-28 05:54:44,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5424929-67b5-4adf-a934-dd96087e11a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:54:44,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5424929-67b5-4adf-a934-dd96087e11a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:54:44,215] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:54:44,215] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 05:54:44,215] [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
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.1833	52	1196	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 05:54:44,217] [INFO] DFAST Taxonomy check result was written to GCA_017965425.1_ASM1796542v1_genomic.fna/tc_result.tsv
[2023-06-28 05:54:44,218] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:54:44,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:54:44,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5424929-67b5-4adf-a934-dd96087e11a6/dqc_reference/checkm_data
[2023-06-28 05:54:44,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:54:44,277] [INFO] Task started: CheckM
[2023-06-28 05:54:44,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017965425.1_ASM1796542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017965425.1_ASM1796542v1_genomic.fna/checkm_input GCA_017965425.1_ASM1796542v1_genomic.fna/checkm_result
[2023-06-28 05:55:51,479] [INFO] Task succeeded: CheckM
[2023-06-28 05:55:51,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 05:55:51,509] [INFO] ===== Completeness check finished =====
[2023-06-28 05:55:51,509] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:55:51,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017965425.1_ASM1796542v1_genomic.fna/markers.fasta)
[2023-06-28 05:55:51,510] [INFO] Task started: Blastn
[2023-06-28 05:55:51,510] [INFO] Running command: blastn -query GCA_017965425.1_ASM1796542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5424929-67b5-4adf-a934-dd96087e11a6/dqc_reference/reference_markers_gtdb.fasta -out GCA_017965425.1_ASM1796542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:55:52,432] [INFO] Task succeeded: Blastn
[2023-06-28 05:55:52,438] [INFO] Selected 19 target genomes.
[2023-06-28 05:55:52,438] [INFO] Target genome list was writen to GCA_017965425.1_ASM1796542v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:55:52,446] [INFO] Task started: fastANI
[2023-06-28 05:55:52,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f6a2aa3-df8d-4b09-ab93-eb412e2d239d/GCA_017965425.1_ASM1796542v1_genomic.fna.gz --refList GCA_017965425.1_ASM1796542v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017965425.1_ASM1796542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:56:03,126] [INFO] Task succeeded: fastANI
[2023-06-28 05:56:03,155] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:56:03,155] [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_017965425.1	s__UBA4372 sp017965425	100.0	1195	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900316355.1	s__UBA4372 sp900316355	79.7627	314	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.71	97.42	0.94	0.87	3	-
GCA_902771725.1	s__UBA4372 sp902771725	79.6251	366	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779845.1	s__UBA4372 sp902779845	79.1985	292	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.82	95.27	0.82	0.79	4	-
GCA_902779165.1	s__UBA4372 sp902779165	79.1507	296	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.70	97.51	0.80	0.77	4	-
GCA_905233765.1	s__UBA4372 sp905233765	79.1452	249	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318115.1	s__UBA4372 sp900318115	79.0538	325	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.30	96.55	0.83	0.74	7	-
GCA_017470425.1	s__UBA4372 sp017470425	78.6525	238	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.15	97.15	0.50	0.50	2	-
GCA_016280855.1	s__UBA4372 sp016280855	78.6269	274	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017429945.1	s__UBA4372 sp017429945	78.6148	241	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017535725.1	s__UBA4372 sp017535725	78.6051	250	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017455585.1	s__UBA4372 sp017455585	78.5148	296	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236985.1	s__UBA4372 sp905236985	78.043	240	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783885.1	s__UBA4372 sp902783885	78.0036	217	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803195.1	s__UBA4372 sp902803195	77.9893	224	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760315.1	s__Prevotella sp902760315	76.4435	63	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291495.1	s__Prevotella sp016291495	76.421	52	1196	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:56:03,157] [INFO] GTDB search result was written to GCA_017965425.1_ASM1796542v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:56:03,158] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:56:03,161] [INFO] DFAST_QC result json was written to GCA_017965425.1_ASM1796542v1_genomic.fna/dqc_result.json
[2023-06-28 05:56:03,161] [INFO] DFAST_QC completed!
[2023-06-28 05:56:03,161] [INFO] Total running time: 0h1m59s