[2023-06-29 04:01:43,555] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:01:43,557] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:01:43,557] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c33538f-f204-4935-aca8-76669936b8e1/dqc_reference
[2023-06-29 04:01:44,697] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:01:44,698] [INFO] Task started: Prodigal
[2023-06-29 04:01:44,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg354b7c2b-9a2d-4d26-8b37-2994bdcfe706/GCA_005790565.1_ASM579056v1_genomic.fna.gz | prodigal -d GCA_005790565.1_ASM579056v1_genomic.fna/cds.fna -a GCA_005790565.1_ASM579056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:01:52,974] [INFO] Task succeeded: Prodigal
[2023-06-29 04:01:52,974] [INFO] Task started: HMMsearch
[2023-06-29 04:01:52,974] [INFO] Running command: hmmsearch --tblout GCA_005790565.1_ASM579056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c33538f-f204-4935-aca8-76669936b8e1/dqc_reference/reference_markers.hmm GCA_005790565.1_ASM579056v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:01:53,157] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:01:53,160] [INFO] Found 6/6 markers.
[2023-06-29 04:01:53,187] [INFO] Query marker FASTA was written to GCA_005790565.1_ASM579056v1_genomic.fna/markers.fasta
[2023-06-29 04:01:53,188] [INFO] Task started: Blastn
[2023-06-29 04:01:53,188] [INFO] Running command: blastn -query GCA_005790565.1_ASM579056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c33538f-f204-4935-aca8-76669936b8e1/dqc_reference/reference_markers.fasta -out GCA_005790565.1_ASM579056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:01:53,775] [INFO] Task succeeded: Blastn
[2023-06-29 04:01:53,779] [INFO] Selected 23 target genomes.
[2023-06-29 04:01:53,779] [INFO] Target genome list was writen to GCA_005790565.1_ASM579056v1_genomic.fna/target_genomes.txt
[2023-06-29 04:01:53,784] [INFO] Task started: fastANI
[2023-06-29 04:01:53,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg354b7c2b-9a2d-4d26-8b37-2994bdcfe706/GCA_005790565.1_ASM579056v1_genomic.fna.gz --refList GCA_005790565.1_ASM579056v1_genomic.fna/target_genomes.txt --output GCA_005790565.1_ASM579056v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:02:12,969] [INFO] Task succeeded: fastANI
[2023-06-29 04:02:12,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c33538f-f204-4935-aca8-76669936b8e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:02:12,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c33538f-f204-4935-aca8-76669936b8e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:02:12,973] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:02:12,973] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 04:02:12,973] [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
--------------------------------------------------------------------------------
[2023-06-29 04:02:12,974] [INFO] DFAST Taxonomy check result was written to GCA_005790565.1_ASM579056v1_genomic.fna/tc_result.tsv
[2023-06-29 04:02:12,975] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:02:12,975] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:02:12,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c33538f-f204-4935-aca8-76669936b8e1/dqc_reference/checkm_data
[2023-06-29 04:02:12,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:02:13,005] [INFO] Task started: CheckM
[2023-06-29 04:02:13,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005790565.1_ASM579056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005790565.1_ASM579056v1_genomic.fna/checkm_input GCA_005790565.1_ASM579056v1_genomic.fna/checkm_result
[2023-06-29 04:02:43,009] [INFO] Task succeeded: CheckM
[2023-06-29 04:02:43,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:02:43,031] [INFO] ===== Completeness check finished =====
[2023-06-29 04:02:43,031] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:02:43,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005790565.1_ASM579056v1_genomic.fna/markers.fasta)
[2023-06-29 04:02:43,032] [INFO] Task started: Blastn
[2023-06-29 04:02:43,032] [INFO] Running command: blastn -query GCA_005790565.1_ASM579056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c33538f-f204-4935-aca8-76669936b8e1/dqc_reference/reference_markers_gtdb.fasta -out GCA_005790565.1_ASM579056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:02:43,749] [INFO] Task succeeded: Blastn
[2023-06-29 04:02:43,753] [INFO] Selected 18 target genomes.
[2023-06-29 04:02:43,753] [INFO] Target genome list was writen to GCA_005790565.1_ASM579056v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:02:43,758] [INFO] Task started: fastANI
[2023-06-29 04:02:43,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg354b7c2b-9a2d-4d26-8b37-2994bdcfe706/GCA_005790565.1_ASM579056v1_genomic.fna.gz --refList GCA_005790565.1_ASM579056v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005790565.1_ASM579056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:02:53,072] [INFO] Task succeeded: fastANI
[2023-06-29 04:02:53,082] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 04:02:53,082] [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_005790565.1	s__F1-140-MAGs142 sp005790565	100.0	794	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-140-MAGs142	95.0	99.70	99.68	0.89	0.89	4	conclusive
GCA_005790605.1	s__F1-140-MAGs142 sp005790605	79.0495	442	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-140-MAGs142	95.0	99.95	99.95	0.96	0.96	2	-
GCA_009691805.1	s__F1-140-MAGs142 sp009691805	77.8953	365	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-140-MAGs142	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671055.1	s__F1-140-MAGs142 sp003671055	77.3183	288	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-140-MAGs142	95.0	99.26	99.00	0.90	0.89	3	-
GCA_903891095.1	s__QWPT01 sp903891095	76.3617	106	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	99.40	98.92	0.94	0.91	5	-
GCA_003671075.1	s__QWPT01 sp003671075	76.2201	74	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	98.44	97.81	0.89	0.84	6	-
GCA_016795035.1	s__JAEUIT01 sp016795035	75.7977	50	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__JAEUIT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124975.1	s__QWPT01 sp016124975	75.7658	96	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671025.1	s__QWPT01 sp003671025	75.6973	79	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	99.38	99.11	0.93	0.92	3	-
GCA_903911205.1	s__QWPT01 sp903911205	75.5827	74	805	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:02:53,083] [INFO] GTDB search result was written to GCA_005790565.1_ASM579056v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:02:53,084] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:02:53,086] [INFO] DFAST_QC result json was written to GCA_005790565.1_ASM579056v1_genomic.fna/dqc_result.json
[2023-06-29 04:02:53,086] [INFO] DFAST_QC completed!
[2023-06-29 04:02:53,086] [INFO] Total running time: 0h1m10s