[2023-06-08 15:04:42,453] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:04:42,456] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:04:42,457] [INFO] DQC Reference Directory: /var/lib/cwl/stg42353982-5e46-4edd-b71d-8a58e3f3e522/dqc_reference
[2023-06-08 15:04:43,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:04:43,762] [INFO] Task started: Prodigal
[2023-06-08 15:04:43,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f571e20-9db9-4b22-919b-085877563cbc/GCA_945897175.1_MsE-01oct19-74_genomic.fna.gz | prodigal -d GCA_945897175.1_MsE-01oct19-74_genomic.fna/cds.fna -a GCA_945897175.1_MsE-01oct19-74_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:04:58,277] [INFO] Task succeeded: Prodigal
[2023-06-08 15:04:58,277] [INFO] Task started: HMMsearch
[2023-06-08 15:04:58,278] [INFO] Running command: hmmsearch --tblout GCA_945897175.1_MsE-01oct19-74_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42353982-5e46-4edd-b71d-8a58e3f3e522/dqc_reference/reference_markers.hmm GCA_945897175.1_MsE-01oct19-74_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:04:58,504] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:04:58,505] [INFO] Found 6/6 markers.
[2023-06-08 15:04:58,530] [INFO] Query marker FASTA was written to GCA_945897175.1_MsE-01oct19-74_genomic.fna/markers.fasta
[2023-06-08 15:04:58,531] [INFO] Task started: Blastn
[2023-06-08 15:04:58,531] [INFO] Running command: blastn -query GCA_945897175.1_MsE-01oct19-74_genomic.fna/markers.fasta -db /var/lib/cwl/stg42353982-5e46-4edd-b71d-8a58e3f3e522/dqc_reference/reference_markers.fasta -out GCA_945897175.1_MsE-01oct19-74_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:04:59,136] [INFO] Task succeeded: Blastn
[2023-06-08 15:04:59,141] [INFO] Selected 15 target genomes.
[2023-06-08 15:04:59,141] [INFO] Target genome list was writen to GCA_945897175.1_MsE-01oct19-74_genomic.fna/target_genomes.txt
[2023-06-08 15:04:59,145] [INFO] Task started: fastANI
[2023-06-08 15:04:59,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f571e20-9db9-4b22-919b-085877563cbc/GCA_945897175.1_MsE-01oct19-74_genomic.fna.gz --refList GCA_945897175.1_MsE-01oct19-74_genomic.fna/target_genomes.txt --output GCA_945897175.1_MsE-01oct19-74_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:05:12,988] [INFO] Task succeeded: fastANI
[2023-06-08 15:05:12,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42353982-5e46-4edd-b71d-8a58e3f3e522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:05:12,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42353982-5e46-4edd-b71d-8a58e3f3e522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:05:12,995] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:05:12,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 15:05:12,996] [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
Terrimicrobium sacchariphilum	strain=NM-5	GCA_001613545.1	690879	690879	type	True	76.4606	53	682	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 15:05:12,998] [INFO] DFAST Taxonomy check result was written to GCA_945897175.1_MsE-01oct19-74_genomic.fna/tc_result.tsv
[2023-06-08 15:05:12,999] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:05:12,999] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:05:12,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42353982-5e46-4edd-b71d-8a58e3f3e522/dqc_reference/checkm_data
[2023-06-08 15:05:13,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:05:13,031] [INFO] Task started: CheckM
[2023-06-08 15:05:13,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945897175.1_MsE-01oct19-74_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945897175.1_MsE-01oct19-74_genomic.fna/checkm_input GCA_945897175.1_MsE-01oct19-74_genomic.fna/checkm_result
[2023-06-08 15:05:57,109] [INFO] Task succeeded: CheckM
[2023-06-08 15:05:57,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 15:05:57,129] [INFO] ===== Completeness check finished =====
[2023-06-08 15:05:57,130] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:05:57,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945897175.1_MsE-01oct19-74_genomic.fna/markers.fasta)
[2023-06-08 15:05:57,130] [INFO] Task started: Blastn
[2023-06-08 15:05:57,131] [INFO] Running command: blastn -query GCA_945897175.1_MsE-01oct19-74_genomic.fna/markers.fasta -db /var/lib/cwl/stg42353982-5e46-4edd-b71d-8a58e3f3e522/dqc_reference/reference_markers_gtdb.fasta -out GCA_945897175.1_MsE-01oct19-74_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:05:58,004] [INFO] Task succeeded: Blastn
[2023-06-08 15:05:58,009] [INFO] Selected 11 target genomes.
[2023-06-08 15:05:58,009] [INFO] Target genome list was writen to GCA_945897175.1_MsE-01oct19-74_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:05:58,016] [INFO] Task started: fastANI
[2023-06-08 15:05:58,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f571e20-9db9-4b22-919b-085877563cbc/GCA_945897175.1_MsE-01oct19-74_genomic.fna.gz --refList GCA_945897175.1_MsE-01oct19-74_genomic.fna/target_genomes_gtdb.txt --output GCA_945897175.1_MsE-01oct19-74_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:06:04,225] [INFO] Task succeeded: fastANI
[2023-06-08 15:06:04,237] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 15:06:04,237] [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_002290555.1	s__UBA967 sp002290555	96.0255	432	682	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	99.67	99.67	0.84	0.84	2	conclusive
GCA_002396485.1	s__UBA967 sp002396485	82.085	434	682	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886045.1	s__UBA967 sp009886045	80.2127	316	682	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402345.1	s__UBA967 sp018402345	78.0081	186	682	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970255.1	s__UBA967 sp018970255	77.9847	171	682	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903915315.1	s__UBA967 sp903915315	77.8091	79	682	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280915.1	s__QYQL01 sp007280915	76.4146	69	682	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__QYQL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003054655.1	s__Terrimicrobium sp003054655	76.3233	50	682	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__Terrimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 15:06:04,240] [INFO] GTDB search result was written to GCA_945897175.1_MsE-01oct19-74_genomic.fna/result_gtdb.tsv
[2023-06-08 15:06:04,240] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:06:04,243] [INFO] DFAST_QC result json was written to GCA_945897175.1_MsE-01oct19-74_genomic.fna/dqc_result.json
[2023-06-08 15:06:04,243] [INFO] DFAST_QC completed!
[2023-06-08 15:06:04,243] [INFO] Total running time: 0h1m22s