[2023-06-27 10:19:50,085] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:19:50,090] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:19:50,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ae8fb6f-481b-452a-a0d8-aac2411149e0/dqc_reference
[2023-06-27 10:19:52,363] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:19:52,364] [INFO] Task started: Prodigal
[2023-06-27 10:19:52,364] [INFO] Running command: gunzip -c /var/lib/cwl/stgc24df53d-6bcb-47bf-b0f5-bf6d70e24b09/GCA_027336285.1_ASM2733628v1_genomic.fna.gz | prodigal -d GCA_027336285.1_ASM2733628v1_genomic.fna/cds.fna -a GCA_027336285.1_ASM2733628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:19:57,573] [INFO] Task succeeded: Prodigal
[2023-06-27 10:19:57,574] [INFO] Task started: HMMsearch
[2023-06-27 10:19:57,574] [INFO] Running command: hmmsearch --tblout GCA_027336285.1_ASM2733628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ae8fb6f-481b-452a-a0d8-aac2411149e0/dqc_reference/reference_markers.hmm GCA_027336285.1_ASM2733628v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:19:57,782] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:19:57,783] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc24df53d-6bcb-47bf-b0f5-bf6d70e24b09/GCA_027336285.1_ASM2733628v1_genomic.fna.gz]
[2023-06-27 10:19:57,838] [INFO] Query marker FASTA was written to GCA_027336285.1_ASM2733628v1_genomic.fna/markers.fasta
[2023-06-27 10:19:57,839] [INFO] Task started: Blastn
[2023-06-27 10:19:57,839] [INFO] Running command: blastn -query GCA_027336285.1_ASM2733628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ae8fb6f-481b-452a-a0d8-aac2411149e0/dqc_reference/reference_markers.fasta -out GCA_027336285.1_ASM2733628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:19:58,627] [INFO] Task succeeded: Blastn
[2023-06-27 10:19:58,632] [INFO] Selected 18 target genomes.
[2023-06-27 10:19:58,633] [INFO] Target genome list was writen to GCA_027336285.1_ASM2733628v1_genomic.fna/target_genomes.txt
[2023-06-27 10:19:58,639] [INFO] Task started: fastANI
[2023-06-27 10:19:58,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgc24df53d-6bcb-47bf-b0f5-bf6d70e24b09/GCA_027336285.1_ASM2733628v1_genomic.fna.gz --refList GCA_027336285.1_ASM2733628v1_genomic.fna/target_genomes.txt --output GCA_027336285.1_ASM2733628v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:20:13,239] [INFO] Task succeeded: fastANI
[2023-06-27 10:20:13,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ae8fb6f-481b-452a-a0d8-aac2411149e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:20:13,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ae8fb6f-481b-452a-a0d8-aac2411149e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:20:13,254] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:20:13,254] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 10:20:13,254] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.0555	69	345	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	75.7956	56	345	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.6606	60	345	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	75.126	55	345	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	75.1014	57	345	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	75.0532	50	345	95	below_threshold
Streptomyces mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	75.0259	53	345	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	74.853	56	345	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	74.853	56	345	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 10:20:13,256] [INFO] DFAST Taxonomy check result was written to GCA_027336285.1_ASM2733628v1_genomic.fna/tc_result.tsv
[2023-06-27 10:20:13,257] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:20:13,257] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:20:13,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ae8fb6f-481b-452a-a0d8-aac2411149e0/dqc_reference/checkm_data
[2023-06-27 10:20:13,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:20:13,289] [INFO] Task started: CheckM
[2023-06-27 10:20:13,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027336285.1_ASM2733628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027336285.1_ASM2733628v1_genomic.fna/checkm_input GCA_027336285.1_ASM2733628v1_genomic.fna/checkm_result
[2023-06-27 10:20:35,242] [INFO] Task succeeded: CheckM
[2023-06-27 10:20:35,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 10:20:35,269] [INFO] ===== Completeness check finished =====
[2023-06-27 10:20:35,269] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:20:35,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027336285.1_ASM2733628v1_genomic.fna/markers.fasta)
[2023-06-27 10:20:35,272] [INFO] Task started: Blastn
[2023-06-27 10:20:35,272] [INFO] Running command: blastn -query GCA_027336285.1_ASM2733628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ae8fb6f-481b-452a-a0d8-aac2411149e0/dqc_reference/reference_markers_gtdb.fasta -out GCA_027336285.1_ASM2733628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:20:35,930] [INFO] Task succeeded: Blastn
[2023-06-27 10:20:35,959] [INFO] Selected 18 target genomes.
[2023-06-27 10:20:35,959] [INFO] Target genome list was writen to GCA_027336285.1_ASM2733628v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:20:35,969] [INFO] Task started: fastANI
[2023-06-27 10:20:35,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgc24df53d-6bcb-47bf-b0f5-bf6d70e24b09/GCA_027336285.1_ASM2733628v1_genomic.fna.gz --refList GCA_027336285.1_ASM2733628v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027336285.1_ASM2733628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:20:47,566] [INFO] Task succeeded: fastANI
[2023-06-27 10:20:47,576] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 10:20:47,576] [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_003159795.1	s__Bog-793 sp003159795	77.1632	64	345	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Bog-793	95.0	99.80	99.71	0.91	0.89	3	-
GCA_003155135.1	s__Bog-515 sp003155135	76.8604	54	345	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-515	95.0	99.89	99.76	0.97	0.95	17	-
GCA_004366205.1	s__SIRW01 sp004366205	75.8465	75	345	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	75.5466	80	345	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995215.1	s__Amycolatopsis azurea	74.853	56	345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-27 10:20:47,578] [INFO] GTDB search result was written to GCA_027336285.1_ASM2733628v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:20:47,579] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:20:47,587] [INFO] DFAST_QC result json was written to GCA_027336285.1_ASM2733628v1_genomic.fna/dqc_result.json
[2023-06-27 10:20:47,588] [INFO] DFAST_QC completed!
[2023-06-27 10:20:47,588] [INFO] Total running time: 0h0m58s