[2023-06-05 23:28:34,089] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:28:34,093] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:28:34,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg735d06c4-f972-4f9c-8d60-d24cd7268edb/dqc_reference
[2023-06-05 23:28:36,762] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:28:36,763] [INFO] Task started: Prodigal
[2023-06-05 23:28:36,763] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc080c59-6ce2-45fa-a25a-8f4b5e39cc4e/GCA_001787005.1_ASM178700v1_genomic.fna.gz | prodigal -d GCA_001787005.1_ASM178700v1_genomic.fna/cds.fna -a GCA_001787005.1_ASM178700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:28:40,924] [INFO] Task succeeded: Prodigal
[2023-06-05 23:28:40,925] [INFO] Task started: HMMsearch
[2023-06-05 23:28:40,925] [INFO] Running command: hmmsearch --tblout GCA_001787005.1_ASM178700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg735d06c4-f972-4f9c-8d60-d24cd7268edb/dqc_reference/reference_markers.hmm GCA_001787005.1_ASM178700v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:28:41,248] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:28:41,250] [INFO] Found 6/6 markers.
[2023-06-05 23:28:41,263] [INFO] Query marker FASTA was written to GCA_001787005.1_ASM178700v1_genomic.fna/markers.fasta
[2023-06-05 23:28:41,264] [INFO] Task started: Blastn
[2023-06-05 23:28:41,264] [INFO] Running command: blastn -query GCA_001787005.1_ASM178700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg735d06c4-f972-4f9c-8d60-d24cd7268edb/dqc_reference/reference_markers.fasta -out GCA_001787005.1_ASM178700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:28:42,394] [INFO] Task succeeded: Blastn
[2023-06-05 23:28:42,398] [INFO] Selected 6 target genomes.
[2023-06-05 23:28:42,399] [INFO] Target genome list was writen to GCA_001787005.1_ASM178700v1_genomic.fna/target_genomes.txt
[2023-06-05 23:28:42,401] [INFO] Task started: fastANI
[2023-06-05 23:28:42,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc080c59-6ce2-45fa-a25a-8f4b5e39cc4e/GCA_001787005.1_ASM178700v1_genomic.fna.gz --refList GCA_001787005.1_ASM178700v1_genomic.fna/target_genomes.txt --output GCA_001787005.1_ASM178700v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:28:45,535] [INFO] Task succeeded: fastANI
[2023-06-05 23:28:45,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg735d06c4-f972-4f9c-8d60-d24cd7268edb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:28:45,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg735d06c4-f972-4f9c-8d60-d24cd7268edb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:28:45,537] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:28:45,538] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 23:28:45,538] [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 23:28:45,540] [INFO] DFAST Taxonomy check result was written to GCA_001787005.1_ASM178700v1_genomic.fna/tc_result.tsv
[2023-06-05 23:28:45,540] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:28:45,540] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:28:45,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg735d06c4-f972-4f9c-8d60-d24cd7268edb/dqc_reference/checkm_data
[2023-06-05 23:28:45,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:28:45,570] [INFO] Task started: CheckM
[2023-06-05 23:28:45,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001787005.1_ASM178700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001787005.1_ASM178700v1_genomic.fna/checkm_input GCA_001787005.1_ASM178700v1_genomic.fna/checkm_result
[2023-06-05 23:29:05,054] [INFO] Task succeeded: CheckM
[2023-06-05 23:29:05,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:29:05,073] [INFO] ===== Completeness check finished =====
[2023-06-05 23:29:05,073] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:29:05,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001787005.1_ASM178700v1_genomic.fna/markers.fasta)
[2023-06-05 23:29:05,074] [INFO] Task started: Blastn
[2023-06-05 23:29:05,074] [INFO] Running command: blastn -query GCA_001787005.1_ASM178700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg735d06c4-f972-4f9c-8d60-d24cd7268edb/dqc_reference/reference_markers_gtdb.fasta -out GCA_001787005.1_ASM178700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:29:06,125] [INFO] Task succeeded: Blastn
[2023-06-05 23:29:06,129] [INFO] Selected 17 target genomes.
[2023-06-05 23:29:06,130] [INFO] Target genome list was writen to GCA_001787005.1_ASM178700v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:29:06,141] [INFO] Task started: fastANI
[2023-06-05 23:29:06,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc080c59-6ce2-45fa-a25a-8f4b5e39cc4e/GCA_001787005.1_ASM178700v1_genomic.fna.gz --refList GCA_001787005.1_ASM178700v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001787005.1_ASM178700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:29:08,771] [INFO] Task succeeded: fastANI
[2023-06-05 23:29:08,776] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 23:29:08,777] [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_001787005.1	s__UBA9973 sp001787005	100.0	264	265	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA9973	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001786745.1	s__UBA9973 sp001786745	76.9323	51	265	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA9973	95.0	99.92	99.90	0.91	0.90	3	-
GCA_001785985.1	s__UBA9973 sp001785985	76.701	50	265	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA9973	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 23:29:08,779] [INFO] GTDB search result was written to GCA_001787005.1_ASM178700v1_genomic.fna/result_gtdb.tsv
[2023-06-05 23:29:08,779] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:29:08,782] [INFO] DFAST_QC result json was written to GCA_001787005.1_ASM178700v1_genomic.fna/dqc_result.json
[2023-06-05 23:29:08,782] [INFO] DFAST_QC completed!
[2023-06-05 23:29:08,783] [INFO] Total running time: 0h0m35s