[2023-06-08 00:03:27,758] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:03:27,826] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:03:27,826] [INFO] DQC Reference Directory: /var/lib/cwl/stgebdefab3-f6b2-4318-9ecf-4d9414b9e108/dqc_reference
[2023-06-08 00:03:31,287] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:03:31,289] [INFO] Task started: Prodigal
[2023-06-08 00:03:31,289] [INFO] Running command: gunzip -c /var/lib/cwl/stg665bd95f-0fd4-4d78-8dcc-a2da1ee43744/GCA_947486155.1_TE-Jun18-53_genomic.fna.gz | prodigal -d GCA_947486155.1_TE-Jun18-53_genomic.fna/cds.fna -a GCA_947486155.1_TE-Jun18-53_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:03:34,232] [INFO] Task succeeded: Prodigal
[2023-06-08 00:03:34,232] [INFO] Task started: HMMsearch
[2023-06-08 00:03:34,232] [INFO] Running command: hmmsearch --tblout GCA_947486155.1_TE-Jun18-53_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebdefab3-f6b2-4318-9ecf-4d9414b9e108/dqc_reference/reference_markers.hmm GCA_947486155.1_TE-Jun18-53_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:03:34,408] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:03:34,410] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg665bd95f-0fd4-4d78-8dcc-a2da1ee43744/GCA_947486155.1_TE-Jun18-53_genomic.fna.gz]
[2023-06-08 00:03:34,423] [INFO] Query marker FASTA was written to GCA_947486155.1_TE-Jun18-53_genomic.fna/markers.fasta
[2023-06-08 00:03:34,424] [INFO] Task started: Blastn
[2023-06-08 00:03:34,424] [INFO] Running command: blastn -query GCA_947486155.1_TE-Jun18-53_genomic.fna/markers.fasta -db /var/lib/cwl/stgebdefab3-f6b2-4318-9ecf-4d9414b9e108/dqc_reference/reference_markers.fasta -out GCA_947486155.1_TE-Jun18-53_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:03:35,741] [INFO] Task succeeded: Blastn
[2023-06-08 00:03:35,767] [INFO] Selected 1 target genomes.
[2023-06-08 00:03:35,768] [INFO] Target genome list was writen to GCA_947486155.1_TE-Jun18-53_genomic.fna/target_genomes.txt
[2023-06-08 00:03:35,770] [INFO] Task started: fastANI
[2023-06-08 00:03:35,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg665bd95f-0fd4-4d78-8dcc-a2da1ee43744/GCA_947486155.1_TE-Jun18-53_genomic.fna.gz --refList GCA_947486155.1_TE-Jun18-53_genomic.fna/target_genomes.txt --output GCA_947486155.1_TE-Jun18-53_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:03:36,485] [INFO] Task succeeded: fastANI
[2023-06-08 00:03:36,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebdefab3-f6b2-4318-9ecf-4d9414b9e108/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:03:36,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebdefab3-f6b2-4318-9ecf-4d9414b9e108/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:03:36,487] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:03:36,487] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:03:36,487] [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
--------------------------------------------------------------------------------
[2023-06-08 00:03:36,494] [INFO] DFAST Taxonomy check result was written to GCA_947486155.1_TE-Jun18-53_genomic.fna/tc_result.tsv
[2023-06-08 00:03:36,496] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:03:36,497] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:03:36,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebdefab3-f6b2-4318-9ecf-4d9414b9e108/dqc_reference/checkm_data
[2023-06-08 00:03:36,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:03:36,514] [INFO] Task started: CheckM
[2023-06-08 00:03:36,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947486155.1_TE-Jun18-53_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947486155.1_TE-Jun18-53_genomic.fna/checkm_input GCA_947486155.1_TE-Jun18-53_genomic.fna/checkm_result
[2023-06-08 00:03:56,473] [INFO] Task succeeded: CheckM
[2023-06-08 00:03:56,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:03:56,495] [INFO] ===== Completeness check finished =====
[2023-06-08 00:03:56,495] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:03:56,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947486155.1_TE-Jun18-53_genomic.fna/markers.fasta)
[2023-06-08 00:03:56,496] [INFO] Task started: Blastn
[2023-06-08 00:03:56,496] [INFO] Running command: blastn -query GCA_947486155.1_TE-Jun18-53_genomic.fna/markers.fasta -db /var/lib/cwl/stgebdefab3-f6b2-4318-9ecf-4d9414b9e108/dqc_reference/reference_markers_gtdb.fasta -out GCA_947486155.1_TE-Jun18-53_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:03:57,211] [INFO] Task succeeded: Blastn
[2023-06-08 00:03:57,245] [INFO] Selected 7 target genomes.
[2023-06-08 00:03:57,246] [INFO] Target genome list was writen to GCA_947486155.1_TE-Jun18-53_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:03:57,253] [INFO] Task started: fastANI
[2023-06-08 00:03:57,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg665bd95f-0fd4-4d78-8dcc-a2da1ee43744/GCA_947486155.1_TE-Jun18-53_genomic.fna.gz --refList GCA_947486155.1_TE-Jun18-53_genomic.fna/target_genomes_gtdb.txt --output GCA_947486155.1_TE-Jun18-53_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:04:00,066] [INFO] Task succeeded: fastANI
[2023-06-08 00:04:00,075] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 00:04:00,075] [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_903914045.1	s__SYAC01 sp903914045	89.6291	180	243	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691785.1	s__SYAC01 sp009691785	86.9897	213	243	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898755.1	s__SYAC01 sp903898755	85.8256	201	243	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	99.48	98.74	0.91	0.88	11	-
GCA_903938205.1	s__SYAC01 sp903938205	85.7553	150	243	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789005.1	s__SYAC01 sp005789005	85.1338	181	243	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831295.1	s__SYAC01 sp903831295	84.9457	199	243	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005787685.1	s__SYAC01 sp005787685	82.4152	194	243	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 00:04:00,078] [INFO] GTDB search result was written to GCA_947486155.1_TE-Jun18-53_genomic.fna/result_gtdb.tsv
[2023-06-08 00:04:00,082] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:04:00,093] [INFO] DFAST_QC result json was written to GCA_947486155.1_TE-Jun18-53_genomic.fna/dqc_result.json
[2023-06-08 00:04:00,094] [INFO] DFAST_QC completed!
[2023-06-08 00:04:00,094] [INFO] Total running time: 0h0m32s