[2023-06-29 04:41:46,799] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:41:46,802] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:41:46,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d0e45c8-265b-43f4-a299-4b561b0ba50e/dqc_reference
[2023-06-29 04:41:48,236] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:41:48,237] [INFO] Task started: Prodigal
[2023-06-29 04:41:48,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg625ee3ff-8d29-41fc-ab88-39112f04edc8/GCA_020439265.1_ASM2043926v1_genomic.fna.gz | prodigal -d GCA_020439265.1_ASM2043926v1_genomic.fna/cds.fna -a GCA_020439265.1_ASM2043926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:41:55,549] [INFO] Task succeeded: Prodigal
[2023-06-29 04:41:55,550] [INFO] Task started: HMMsearch
[2023-06-29 04:41:55,550] [INFO] Running command: hmmsearch --tblout GCA_020439265.1_ASM2043926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d0e45c8-265b-43f4-a299-4b561b0ba50e/dqc_reference/reference_markers.hmm GCA_020439265.1_ASM2043926v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:41:55,787] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:41:55,788] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg625ee3ff-8d29-41fc-ab88-39112f04edc8/GCA_020439265.1_ASM2043926v1_genomic.fna.gz]
[2023-06-29 04:41:55,834] [INFO] Query marker FASTA was written to GCA_020439265.1_ASM2043926v1_genomic.fna/markers.fasta
[2023-06-29 04:41:55,835] [INFO] Task started: Blastn
[2023-06-29 04:41:55,835] [INFO] Running command: blastn -query GCA_020439265.1_ASM2043926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d0e45c8-265b-43f4-a299-4b561b0ba50e/dqc_reference/reference_markers.fasta -out GCA_020439265.1_ASM2043926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:41:56,431] [INFO] Task succeeded: Blastn
[2023-06-29 04:41:56,435] [INFO] Selected 10 target genomes.
[2023-06-29 04:41:56,435] [INFO] Target genome list was writen to GCA_020439265.1_ASM2043926v1_genomic.fna/target_genomes.txt
[2023-06-29 04:41:56,439] [INFO] Task started: fastANI
[2023-06-29 04:41:56,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg625ee3ff-8d29-41fc-ab88-39112f04edc8/GCA_020439265.1_ASM2043926v1_genomic.fna.gz --refList GCA_020439265.1_ASM2043926v1_genomic.fna/target_genomes.txt --output GCA_020439265.1_ASM2043926v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:42:06,459] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:06,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d0e45c8-265b-43f4-a299-4b561b0ba50e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:42:06,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d0e45c8-265b-43f4-a299-4b561b0ba50e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:42:06,468] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:42:06,469] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:42:06,469] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.4005	77	469	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	74.8953	98	469	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	74.8266	128	469	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	74.8212	128	469	95	below_threshold
Actinomycetospora succinea	strain=DSM 45775	GCA_004363095.1	663603	663603	type	True	74.7537	78	469	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	74.7433	65	469	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	74.7418	75	469	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	74.6752	109	469	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:42:06,471] [INFO] DFAST Taxonomy check result was written to GCA_020439265.1_ASM2043926v1_genomic.fna/tc_result.tsv
[2023-06-29 04:42:06,472] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:42:06,472] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:42:06,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d0e45c8-265b-43f4-a299-4b561b0ba50e/dqc_reference/checkm_data
[2023-06-29 04:42:06,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:42:06,504] [INFO] Task started: CheckM
[2023-06-29 04:42:06,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020439265.1_ASM2043926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020439265.1_ASM2043926v1_genomic.fna/checkm_input GCA_020439265.1_ASM2043926v1_genomic.fna/checkm_result
[2023-06-29 04:42:32,047] [INFO] Task succeeded: CheckM
[2023-06-29 04:42:32,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:42:32,070] [INFO] ===== Completeness check finished =====
[2023-06-29 04:42:32,070] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:42:32,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020439265.1_ASM2043926v1_genomic.fna/markers.fasta)
[2023-06-29 04:42:32,071] [INFO] Task started: Blastn
[2023-06-29 04:42:32,071] [INFO] Running command: blastn -query GCA_020439265.1_ASM2043926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d0e45c8-265b-43f4-a299-4b561b0ba50e/dqc_reference/reference_markers_gtdb.fasta -out GCA_020439265.1_ASM2043926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:42:32,875] [INFO] Task succeeded: Blastn
[2023-06-29 04:42:32,880] [INFO] Selected 8 target genomes.
[2023-06-29 04:42:32,880] [INFO] Target genome list was writen to GCA_020439265.1_ASM2043926v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:42:32,882] [INFO] Task started: fastANI
[2023-06-29 04:42:32,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg625ee3ff-8d29-41fc-ab88-39112f04edc8/GCA_020439265.1_ASM2043926v1_genomic.fna.gz --refList GCA_020439265.1_ASM2043926v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020439265.1_ASM2043926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:42:37,048] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:37,127] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:42:37,128] [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_016719385.1	s__Microthrix sp002473265	79.9677	277	469	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__Microthrix	95.0	98.81	98.46	0.90	0.86	7	-
GCF_000299415.1	s__Microthrix parvicella	79.4163	265	469	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__Microthrix	95.0	99.08	98.57	0.94	0.83	22	-
GCA_016649895.1	s__Actinomarinicola sp016649895	75.5908	58	469	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	75.4886	82	469	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121465.1	s__SKKL01 sp007121465	75.3686	54	469	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__SKKL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:42:37,131] [INFO] GTDB search result was written to GCA_020439265.1_ASM2043926v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:42:37,132] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:42:37,136] [INFO] DFAST_QC result json was written to GCA_020439265.1_ASM2043926v1_genomic.fna/dqc_result.json
[2023-06-29 04:42:37,137] [INFO] DFAST_QC completed!
[2023-06-29 04:42:37,137] [INFO] Total running time: 0h0m50s