[2023-06-17 03:01:35,780] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:01:35,795] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:01:35,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg59e2b387-ad78-4a67-b27f-dceb62364821/dqc_reference
[2023-06-17 03:01:37,088] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:01:37,089] [INFO] Task started: Prodigal
[2023-06-17 03:01:37,089] [INFO] Running command: gunzip -c /var/lib/cwl/stg1fb1a7c5-e015-4975-b6d4-3494da3582f1/GCA_028817455.1_ASM2881745v1_genomic.fna.gz | prodigal -d GCA_028817455.1_ASM2881745v1_genomic.fna/cds.fna -a GCA_028817455.1_ASM2881745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:01:47,840] [INFO] Task succeeded: Prodigal
[2023-06-17 03:01:47,840] [INFO] Task started: HMMsearch
[2023-06-17 03:01:47,841] [INFO] Running command: hmmsearch --tblout GCA_028817455.1_ASM2881745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59e2b387-ad78-4a67-b27f-dceb62364821/dqc_reference/reference_markers.hmm GCA_028817455.1_ASM2881745v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:01:48,024] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:01:48,027] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg1fb1a7c5-e015-4975-b6d4-3494da3582f1/GCA_028817455.1_ASM2881745v1_genomic.fna.gz]
[2023-06-17 03:01:48,051] [INFO] Query marker FASTA was written to GCA_028817455.1_ASM2881745v1_genomic.fna/markers.fasta
[2023-06-17 03:01:48,052] [INFO] Task started: Blastn
[2023-06-17 03:01:48,052] [INFO] Running command: blastn -query GCA_028817455.1_ASM2881745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59e2b387-ad78-4a67-b27f-dceb62364821/dqc_reference/reference_markers.fasta -out GCA_028817455.1_ASM2881745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:01:48,547] [INFO] Task succeeded: Blastn
[2023-06-17 03:01:48,552] [INFO] Selected 1 target genomes.
[2023-06-17 03:01:48,553] [INFO] Target genome list was writen to GCA_028817455.1_ASM2881745v1_genomic.fna/target_genomes.txt
[2023-06-17 03:01:48,556] [INFO] Task started: fastANI
[2023-06-17 03:01:48,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fb1a7c5-e015-4975-b6d4-3494da3582f1/GCA_028817455.1_ASM2881745v1_genomic.fna.gz --refList GCA_028817455.1_ASM2881745v1_genomic.fna/target_genomes.txt --output GCA_028817455.1_ASM2881745v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:01:49,161] [INFO] Task succeeded: fastANI
[2023-06-17 03:01:49,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59e2b387-ad78-4a67-b27f-dceb62364821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:01:49,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59e2b387-ad78-4a67-b27f-dceb62364821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:01:49,163] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:01:49,163] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 03:01:49,164] [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 03:01:49,166] [INFO] DFAST Taxonomy check result was written to GCA_028817455.1_ASM2881745v1_genomic.fna/tc_result.tsv
[2023-06-17 03:01:49,167] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:01:49,167] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:01:49,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59e2b387-ad78-4a67-b27f-dceb62364821/dqc_reference/checkm_data
[2023-06-17 03:01:49,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:01:49,196] [INFO] Task started: CheckM
[2023-06-17 03:01:49,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028817455.1_ASM2881745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028817455.1_ASM2881745v1_genomic.fna/checkm_input GCA_028817455.1_ASM2881745v1_genomic.fna/checkm_result
[2023-06-17 03:02:22,221] [INFO] Task succeeded: CheckM
[2023-06-17 03:02:22,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 03:02:22,246] [INFO] ===== Completeness check finished =====
[2023-06-17 03:02:22,246] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:02:22,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028817455.1_ASM2881745v1_genomic.fna/markers.fasta)
[2023-06-17 03:02:22,247] [INFO] Task started: Blastn
[2023-06-17 03:02:22,247] [INFO] Running command: blastn -query GCA_028817455.1_ASM2881745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59e2b387-ad78-4a67-b27f-dceb62364821/dqc_reference/reference_markers_gtdb.fasta -out GCA_028817455.1_ASM2881745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:02:22,711] [INFO] Task succeeded: Blastn
[2023-06-17 03:02:22,715] [INFO] Selected 5 target genomes.
[2023-06-17 03:02:22,716] [INFO] Target genome list was writen to GCA_028817455.1_ASM2881745v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:02:22,722] [INFO] Task started: fastANI
[2023-06-17 03:02:22,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fb1a7c5-e015-4975-b6d4-3494da3582f1/GCA_028817455.1_ASM2881745v1_genomic.fna.gz --refList GCA_028817455.1_ASM2881745v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028817455.1_ASM2881745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:02:24,652] [INFO] Task succeeded: fastANI
[2023-06-17 03:02:24,660] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 03:02:24,660] [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_003724275.1	s__Cenarchaeum sp003724275	98.067	295	526	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Cenarchaeum	95.0	98.62	98.31	0.77	0.75	3	conclusive
GCA_007570915.1	s__Cenarchaeum sp007570915	88.0918	255	526	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Cenarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900620265.1	s__Nitrosopumilus sp900620265	77.449	88	526	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:02:24,663] [INFO] GTDB search result was written to GCA_028817455.1_ASM2881745v1_genomic.fna/result_gtdb.tsv
[2023-06-17 03:02:24,663] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:02:24,666] [INFO] DFAST_QC result json was written to GCA_028817455.1_ASM2881745v1_genomic.fna/dqc_result.json
[2023-06-17 03:02:24,666] [INFO] DFAST_QC completed!
[2023-06-17 03:02:24,667] [INFO] Total running time: 0h0m49s