[2023-06-05 02:26:48,142] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:26:48,144] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:26:48,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ac26bb0-9b64-410f-87e7-a9eb65c91f97/dqc_reference
[2023-06-05 02:26:51,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:26:51,173] [INFO] Task started: Prodigal
[2023-06-05 02:26:51,174] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d2090b0-1643-4d2c-9b46-1bbdc74f5739/GCA_001004005.1_ASM100400v1_genomic.fna.gz | prodigal -d GCA_001004005.1_ASM100400v1_genomic.fna/cds.fna -a GCA_001004005.1_ASM100400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:26:55,730] [INFO] Task succeeded: Prodigal
[2023-06-05 02:26:55,730] [INFO] Task started: HMMsearch
[2023-06-05 02:26:55,731] [INFO] Running command: hmmsearch --tblout GCA_001004005.1_ASM100400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ac26bb0-9b64-410f-87e7-a9eb65c91f97/dqc_reference/reference_markers.hmm GCA_001004005.1_ASM100400v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:26:55,914] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:26:55,916] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9d2090b0-1643-4d2c-9b46-1bbdc74f5739/GCA_001004005.1_ASM100400v1_genomic.fna.gz]
[2023-06-05 02:26:55,930] [INFO] Query marker FASTA was written to GCA_001004005.1_ASM100400v1_genomic.fna/markers.fasta
[2023-06-05 02:26:55,930] [INFO] Task started: Blastn
[2023-06-05 02:26:55,931] [INFO] Running command: blastn -query GCA_001004005.1_ASM100400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ac26bb0-9b64-410f-87e7-a9eb65c91f97/dqc_reference/reference_markers.fasta -out GCA_001004005.1_ASM100400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:26:56,520] [INFO] Task succeeded: Blastn
[2023-06-05 02:26:56,525] [INFO] Selected 16 target genomes.
[2023-06-05 02:26:56,525] [INFO] Target genome list was writen to GCA_001004005.1_ASM100400v1_genomic.fna/target_genomes.txt
[2023-06-05 02:26:56,532] [INFO] Task started: fastANI
[2023-06-05 02:26:56,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d2090b0-1643-4d2c-9b46-1bbdc74f5739/GCA_001004005.1_ASM100400v1_genomic.fna.gz --refList GCA_001004005.1_ASM100400v1_genomic.fna/target_genomes.txt --output GCA_001004005.1_ASM100400v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:27:08,840] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:08,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ac26bb0-9b64-410f-87e7-a9eb65c91f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:27:08,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ac26bb0-9b64-410f-87e7-a9eb65c91f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:27:08,843] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:27:08,843] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:27:08,843] [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
--------------------------------------------------------------------------------
[2023-06-05 02:27:08,846] [INFO] DFAST Taxonomy check result was written to GCA_001004005.1_ASM100400v1_genomic.fna/tc_result.tsv
[2023-06-05 02:27:08,847] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:27:08,847] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:27:08,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ac26bb0-9b64-410f-87e7-a9eb65c91f97/dqc_reference/checkm_data
[2023-06-05 02:27:08,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:27:08,867] [INFO] Task started: CheckM
[2023-06-05 02:27:08,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001004005.1_ASM100400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001004005.1_ASM100400v1_genomic.fna/checkm_input GCA_001004005.1_ASM100400v1_genomic.fna/checkm_result
[2023-06-05 02:27:28,551] [INFO] Task succeeded: CheckM
[2023-06-05 02:27:28,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:27:28,573] [INFO] ===== Completeness check finished =====
[2023-06-05 02:27:28,573] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:27:28,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001004005.1_ASM100400v1_genomic.fna/markers.fasta)
[2023-06-05 02:27:28,574] [INFO] Task started: Blastn
[2023-06-05 02:27:28,574] [INFO] Running command: blastn -query GCA_001004005.1_ASM100400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ac26bb0-9b64-410f-87e7-a9eb65c91f97/dqc_reference/reference_markers_gtdb.fasta -out GCA_001004005.1_ASM100400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:27:29,382] [INFO] Task succeeded: Blastn
[2023-06-05 02:27:29,389] [INFO] Selected 20 target genomes.
[2023-06-05 02:27:29,389] [INFO] Target genome list was writen to GCA_001004005.1_ASM100400v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:27:29,488] [INFO] Task started: fastANI
[2023-06-05 02:27:29,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d2090b0-1643-4d2c-9b46-1bbdc74f5739/GCA_001004005.1_ASM100400v1_genomic.fna.gz --refList GCA_001004005.1_ASM100400v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001004005.1_ASM100400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:27:34,988] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:34,993] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:27:34,993] [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_001004005.1	s__UBA10002 sp001004005	100.0	275	278	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA10002;g__UBA10002	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009694955.1	s__UBA10002 sp009694955	77.654	75	278	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA10002;g__UBA10002	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:27:34,996] [INFO] GTDB search result was written to GCA_001004005.1_ASM100400v1_genomic.fna/result_gtdb.tsv
[2023-06-05 02:27:34,996] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:27:34,999] [INFO] DFAST_QC result json was written to GCA_001004005.1_ASM100400v1_genomic.fna/dqc_result.json
[2023-06-05 02:27:34,999] [INFO] DFAST_QC completed!
[2023-06-05 02:27:34,999] [INFO] Total running time: 0h0m47s