[2023-06-28 17:39:49,649] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:39:49,652] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:39:49,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg5473c9a4-fda0-4144-a2fe-8c7979ac9984/dqc_reference
[2023-06-28 17:39:50,882] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:39:50,884] [INFO] Task started: Prodigal
[2023-06-28 17:39:50,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg5faf1229-39ca-428e-8c69-a737042f38ca/GCA_020200375.1_ASM2020037v1_genomic.fna.gz | prodigal -d GCA_020200375.1_ASM2020037v1_genomic.fna/cds.fna -a GCA_020200375.1_ASM2020037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:40:02,388] [INFO] Task succeeded: Prodigal
[2023-06-28 17:40:02,388] [INFO] Task started: HMMsearch
[2023-06-28 17:40:02,388] [INFO] Running command: hmmsearch --tblout GCA_020200375.1_ASM2020037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5473c9a4-fda0-4144-a2fe-8c7979ac9984/dqc_reference/reference_markers.hmm GCA_020200375.1_ASM2020037v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:40:02,738] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:40:02,740] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5faf1229-39ca-428e-8c69-a737042f38ca/GCA_020200375.1_ASM2020037v1_genomic.fna.gz]
[2023-06-28 17:40:02,810] [INFO] Query marker FASTA was written to GCA_020200375.1_ASM2020037v1_genomic.fna/markers.fasta
[2023-06-28 17:40:02,811] [INFO] Task started: Blastn
[2023-06-28 17:40:02,811] [INFO] Running command: blastn -query GCA_020200375.1_ASM2020037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5473c9a4-fda0-4144-a2fe-8c7979ac9984/dqc_reference/reference_markers.fasta -out GCA_020200375.1_ASM2020037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:40:03,526] [INFO] Task succeeded: Blastn
[2023-06-28 17:40:03,530] [INFO] Selected 25 target genomes.
[2023-06-28 17:40:03,530] [INFO] Target genome list was writen to GCA_020200375.1_ASM2020037v1_genomic.fna/target_genomes.txt
[2023-06-28 17:40:03,534] [INFO] Task started: fastANI
[2023-06-28 17:40:03,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg5faf1229-39ca-428e-8c69-a737042f38ca/GCA_020200375.1_ASM2020037v1_genomic.fna.gz --refList GCA_020200375.1_ASM2020037v1_genomic.fna/target_genomes.txt --output GCA_020200375.1_ASM2020037v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:40:25,359] [INFO] Task succeeded: fastANI
[2023-06-28 17:40:25,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5473c9a4-fda0-4144-a2fe-8c7979ac9984/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:40:25,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5473c9a4-fda0-4144-a2fe-8c7979ac9984/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:40:25,372] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:40:25,372] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:40:25,372] [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
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	74.7756	55	1018	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.7572	96	1018	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	74.7494	51	1018	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	74.6479	54	1018	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	74.6305	50	1018	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:40:25,374] [INFO] DFAST Taxonomy check result was written to GCA_020200375.1_ASM2020037v1_genomic.fna/tc_result.tsv
[2023-06-28 17:40:25,375] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:40:25,375] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:40:25,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5473c9a4-fda0-4144-a2fe-8c7979ac9984/dqc_reference/checkm_data
[2023-06-28 17:40:25,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:40:25,428] [INFO] Task started: CheckM
[2023-06-28 17:40:25,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020200375.1_ASM2020037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020200375.1_ASM2020037v1_genomic.fna/checkm_input GCA_020200375.1_ASM2020037v1_genomic.fna/checkm_result
[2023-06-28 17:41:02,221] [INFO] Task succeeded: CheckM
[2023-06-28 17:41:02,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 26.89%
Strain heterogeneity: 81.82%
--------------------------------------------------------------------------------
[2023-06-28 17:41:02,252] [INFO] ===== Completeness check finished =====
[2023-06-28 17:41:02,252] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:41:02,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020200375.1_ASM2020037v1_genomic.fna/markers.fasta)
[2023-06-28 17:41:02,253] [INFO] Task started: Blastn
[2023-06-28 17:41:02,253] [INFO] Running command: blastn -query GCA_020200375.1_ASM2020037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5473c9a4-fda0-4144-a2fe-8c7979ac9984/dqc_reference/reference_markers_gtdb.fasta -out GCA_020200375.1_ASM2020037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:41:03,273] [INFO] Task succeeded: Blastn
[2023-06-28 17:41:03,279] [INFO] Selected 29 target genomes.
[2023-06-28 17:41:03,279] [INFO] Target genome list was writen to GCA_020200375.1_ASM2020037v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:41:03,296] [INFO] Task started: fastANI
[2023-06-28 17:41:03,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg5faf1229-39ca-428e-8c69-a737042f38ca/GCA_020200375.1_ASM2020037v1_genomic.fna.gz --refList GCA_020200375.1_ASM2020037v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020200375.1_ASM2020037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:41:21,437] [INFO] Task succeeded: fastANI
[2023-06-28 17:41:21,445] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:41:21,446] [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_902806415.1	s__CADCWN01 sp902806415	75.6441	103	1018	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__CADCWN01;g__CADCWN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806325.1	s__CADCWE01 sp902806325	75.5145	61	1018	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__CADCWE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806405.1	s__CADCWL01 sp902806405	75.1252	62	1018	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__CADCWL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:41:21,448] [INFO] GTDB search result was written to GCA_020200375.1_ASM2020037v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:41:21,448] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:41:21,451] [INFO] DFAST_QC result json was written to GCA_020200375.1_ASM2020037v1_genomic.fna/dqc_result.json
[2023-06-28 17:41:21,452] [INFO] DFAST_QC completed!
[2023-06-28 17:41:21,452] [INFO] Total running time: 0h1m32s