[2023-06-17 01:28:53,896] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:28:53,901] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:28:53,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg8015046d-a41e-4ce7-b1f6-401e97a6ff87/dqc_reference
[2023-06-17 01:28:55,299] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:28:55,300] [INFO] Task started: Prodigal
[2023-06-17 01:28:55,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f4df75d-dafa-4d6e-a744-5b66eeeacb2d/GCA_003564385.1_ASM356438v1_genomic.fna.gz | prodigal -d GCA_003564385.1_ASM356438v1_genomic.fna/cds.fna -a GCA_003564385.1_ASM356438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:29:03,887] [INFO] Task succeeded: Prodigal
[2023-06-17 01:29:03,887] [INFO] Task started: HMMsearch
[2023-06-17 01:29:03,887] [INFO] Running command: hmmsearch --tblout GCA_003564385.1_ASM356438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8015046d-a41e-4ce7-b1f6-401e97a6ff87/dqc_reference/reference_markers.hmm GCA_003564385.1_ASM356438v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:29:04,165] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:29:04,166] [INFO] Found 6/6 markers.
[2023-06-17 01:29:04,206] [INFO] Query marker FASTA was written to GCA_003564385.1_ASM356438v1_genomic.fna/markers.fasta
[2023-06-17 01:29:04,207] [INFO] Task started: Blastn
[2023-06-17 01:29:04,207] [INFO] Running command: blastn -query GCA_003564385.1_ASM356438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8015046d-a41e-4ce7-b1f6-401e97a6ff87/dqc_reference/reference_markers.fasta -out GCA_003564385.1_ASM356438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:29:04,856] [INFO] Task succeeded: Blastn
[2023-06-17 01:29:04,860] [INFO] Selected 23 target genomes.
[2023-06-17 01:29:04,861] [INFO] Target genome list was writen to GCA_003564385.1_ASM356438v1_genomic.fna/target_genomes.txt
[2023-06-17 01:29:04,882] [INFO] Task started: fastANI
[2023-06-17 01:29:04,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f4df75d-dafa-4d6e-a744-5b66eeeacb2d/GCA_003564385.1_ASM356438v1_genomic.fna.gz --refList GCA_003564385.1_ASM356438v1_genomic.fna/target_genomes.txt --output GCA_003564385.1_ASM356438v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:29:23,286] [INFO] Task succeeded: fastANI
[2023-06-17 01:29:23,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8015046d-a41e-4ce7-b1f6-401e97a6ff87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:29:23,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8015046d-a41e-4ce7-b1f6-401e97a6ff87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:29:23,289] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:29:23,290] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 01:29:23,290] [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
--------------------------------------------------------------------------------
[2023-06-17 01:29:23,292] [INFO] DFAST Taxonomy check result was written to GCA_003564385.1_ASM356438v1_genomic.fna/tc_result.tsv
[2023-06-17 01:29:23,293] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:29:23,293] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:29:23,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8015046d-a41e-4ce7-b1f6-401e97a6ff87/dqc_reference/checkm_data
[2023-06-17 01:29:23,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:29:23,334] [INFO] Task started: CheckM
[2023-06-17 01:29:23,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003564385.1_ASM356438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003564385.1_ASM356438v1_genomic.fna/checkm_input GCA_003564385.1_ASM356438v1_genomic.fna/checkm_result
[2023-06-17 01:29:54,084] [INFO] Task succeeded: CheckM
[2023-06-17 01:29:54,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:29:54,112] [INFO] ===== Completeness check finished =====
[2023-06-17 01:29:54,112] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:29:54,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003564385.1_ASM356438v1_genomic.fna/markers.fasta)
[2023-06-17 01:29:54,113] [INFO] Task started: Blastn
[2023-06-17 01:29:54,113] [INFO] Running command: blastn -query GCA_003564385.1_ASM356438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8015046d-a41e-4ce7-b1f6-401e97a6ff87/dqc_reference/reference_markers_gtdb.fasta -out GCA_003564385.1_ASM356438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:29:54,967] [INFO] Task succeeded: Blastn
[2023-06-17 01:29:54,972] [INFO] Selected 18 target genomes.
[2023-06-17 01:29:54,973] [INFO] Target genome list was writen to GCA_003564385.1_ASM356438v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:29:54,988] [INFO] Task started: fastANI
[2023-06-17 01:29:54,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f4df75d-dafa-4d6e-a744-5b66eeeacb2d/GCA_003564385.1_ASM356438v1_genomic.fna.gz --refList GCA_003564385.1_ASM356438v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003564385.1_ASM356438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:30:06,582] [INFO] Task succeeded: fastANI
[2023-06-17 01:30:06,594] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:30:06,594] [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_003562335.1	s__SLLF01 sp003562335	99.6675	646	833	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__SLAD01;f__SLAD01;g__SLLF01	95.0	99.61	99.52	0.90	0.88	3	conclusive
GCA_007134175.1	s__SLLF01 sp007134175	77.427	134	833	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__SLAD01;f__SLAD01;g__SLLF01	95.0	98.65	98.65	0.75	0.75	2	-
GCA_007136425.1	s__SKZA01 sp007136425	77.1888	53	833	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__SLAD01;f__SLAD01;g__SKZA01	95.0	99.49	99.06	0.89	0.87	5	-
GCA_007128275.1	s__SKZA01 sp007128275	76.3974	60	833	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__SLAD01;f__SLAD01;g__SKZA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123265.1	s__SLAD01 sp007123265	76.1609	52	833	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__SLAD01;f__SLAD01;g__SLAD01	95.0	99.48	99.34	0.85	0.79	4	-
--------------------------------------------------------------------------------
[2023-06-17 01:30:06,597] [INFO] GTDB search result was written to GCA_003564385.1_ASM356438v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:30:06,597] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:30:06,601] [INFO] DFAST_QC result json was written to GCA_003564385.1_ASM356438v1_genomic.fna/dqc_result.json
[2023-06-17 01:30:06,601] [INFO] DFAST_QC completed!
[2023-06-17 01:30:06,601] [INFO] Total running time: 0h1m13s