[2023-06-13 16:35:22,328] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:35:22,331] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:35:22,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg55814c1a-2dc7-479f-b959-c3921be7fbcc/dqc_reference
[2023-06-13 16:35:23,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:35:23,620] [INFO] Task started: Prodigal
[2023-06-13 16:35:23,620] [INFO] Running command: gunzip -c /var/lib/cwl/stge7ad747f-9ecd-44dd-9685-4f403da05edb/GCA_947449455.1_Jr-20nov17-61_genomic.fna.gz | prodigal -d GCA_947449455.1_Jr-20nov17-61_genomic.fna/cds.fna -a GCA_947449455.1_Jr-20nov17-61_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:35:36,272] [INFO] Task succeeded: Prodigal
[2023-06-13 16:35:36,272] [INFO] Task started: HMMsearch
[2023-06-13 16:35:36,273] [INFO] Running command: hmmsearch --tblout GCA_947449455.1_Jr-20nov17-61_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55814c1a-2dc7-479f-b959-c3921be7fbcc/dqc_reference/reference_markers.hmm GCA_947449455.1_Jr-20nov17-61_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:35:36,486] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:35:36,487] [INFO] Found 6/6 markers.
[2023-06-13 16:35:36,515] [INFO] Query marker FASTA was written to GCA_947449455.1_Jr-20nov17-61_genomic.fna/markers.fasta
[2023-06-13 16:35:36,516] [INFO] Task started: Blastn
[2023-06-13 16:35:36,516] [INFO] Running command: blastn -query GCA_947449455.1_Jr-20nov17-61_genomic.fna/markers.fasta -db /var/lib/cwl/stg55814c1a-2dc7-479f-b959-c3921be7fbcc/dqc_reference/reference_markers.fasta -out GCA_947449455.1_Jr-20nov17-61_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:35:37,149] [INFO] Task succeeded: Blastn
[2023-06-13 16:35:37,156] [INFO] Selected 22 target genomes.
[2023-06-13 16:35:37,157] [INFO] Target genome list was writen to GCA_947449455.1_Jr-20nov17-61_genomic.fna/target_genomes.txt
[2023-06-13 16:35:37,160] [INFO] Task started: fastANI
[2023-06-13 16:35:37,160] [INFO] Running command: fastANI --query /var/lib/cwl/stge7ad747f-9ecd-44dd-9685-4f403da05edb/GCA_947449455.1_Jr-20nov17-61_genomic.fna.gz --refList GCA_947449455.1_Jr-20nov17-61_genomic.fna/target_genomes.txt --output GCA_947449455.1_Jr-20nov17-61_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:35:53,963] [INFO] Task succeeded: fastANI
[2023-06-13 16:35:53,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55814c1a-2dc7-479f-b959-c3921be7fbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:35:53,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55814c1a-2dc7-479f-b959-c3921be7fbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:35:53,966] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:35:53,966] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 16:35:53,966] [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
--------------------------------------------------------------------------------
[2023-06-13 16:35:53,969] [INFO] DFAST Taxonomy check result was written to GCA_947449455.1_Jr-20nov17-61_genomic.fna/tc_result.tsv
[2023-06-13 16:35:53,970] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:35:53,970] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:35:53,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55814c1a-2dc7-479f-b959-c3921be7fbcc/dqc_reference/checkm_data
[2023-06-13 16:35:53,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:35:54,005] [INFO] Task started: CheckM
[2023-06-13 16:35:54,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947449455.1_Jr-20nov17-61_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947449455.1_Jr-20nov17-61_genomic.fna/checkm_input GCA_947449455.1_Jr-20nov17-61_genomic.fna/checkm_result
[2023-06-13 16:36:32,499] [INFO] Task succeeded: CheckM
[2023-06-13 16:36:32,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 16:36:32,525] [INFO] ===== Completeness check finished =====
[2023-06-13 16:36:32,525] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:36:32,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947449455.1_Jr-20nov17-61_genomic.fna/markers.fasta)
[2023-06-13 16:36:32,526] [INFO] Task started: Blastn
[2023-06-13 16:36:32,526] [INFO] Running command: blastn -query GCA_947449455.1_Jr-20nov17-61_genomic.fna/markers.fasta -db /var/lib/cwl/stg55814c1a-2dc7-479f-b959-c3921be7fbcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_947449455.1_Jr-20nov17-61_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:36:33,433] [INFO] Task succeeded: Blastn
[2023-06-13 16:36:33,437] [INFO] Selected 14 target genomes.
[2023-06-13 16:36:33,437] [INFO] Target genome list was writen to GCA_947449455.1_Jr-20nov17-61_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:36:33,440] [INFO] Task started: fastANI
[2023-06-13 16:36:33,440] [INFO] Running command: fastANI --query /var/lib/cwl/stge7ad747f-9ecd-44dd-9685-4f403da05edb/GCA_947449455.1_Jr-20nov17-61_genomic.fna.gz --refList GCA_947449455.1_Jr-20nov17-61_genomic.fna/target_genomes_gtdb.txt --output GCA_947449455.1_Jr-20nov17-61_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:36:39,182] [INFO] Task succeeded: fastANI
[2023-06-13 16:36:39,197] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 16:36:39,197] [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_903855995.1	s__UBA953 sp903855995	99.4097	691	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.61	99.32	0.98	0.94	20	conclusive
GCA_903879465.1	s__UBA953 sp903879465	85.9261	279	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853185.1	s__UBA953 sp903853185	83.182	297	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	98.54	98.54	0.77	0.77	2	-
GCA_009924535.1	s__UBA953 sp009924535	83.1319	306	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569165.1	s__UBA953 sp003569165	83.0194	432	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293385.1	s__UBA953 sp004293385	82.9591	210	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903829855.1	s__UBA953 sp903829855	82.8122	392	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.27	99.00	0.85	0.74	14	-
GCA_002293125.1	s__UBA953 sp002293125	82.7507	439	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.83	99.83	0.93	0.93	2	-
GCA_016871725.1	s__UBA953 sp016871725	82.2161	453	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889525.1	s__UBA953 sp903889525	82.1123	439	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917805.1	s__UBA953 sp009917805	81.9671	293	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831005.1	s__UBA953 sp903831005	81.357	268	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014193315.1	s__UBA953 sp003569405	80.3489	383	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.72	96.62	0.94	0.91	4	-
GCA_002293065.1	s__UBA953 sp002293065	79.8824	301	711	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.98	96.04	0.82	0.76	4	-
--------------------------------------------------------------------------------
[2023-06-13 16:36:39,200] [INFO] GTDB search result was written to GCA_947449455.1_Jr-20nov17-61_genomic.fna/result_gtdb.tsv
[2023-06-13 16:36:39,201] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:36:39,204] [INFO] DFAST_QC result json was written to GCA_947449455.1_Jr-20nov17-61_genomic.fna/dqc_result.json
[2023-06-13 16:36:39,204] [INFO] DFAST_QC completed!
[2023-06-13 16:36:39,204] [INFO] Total running time: 0h1m17s