[2024-01-25 19:01:20,696] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:20,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:20,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg64e17ee4-cf61-41ff-8dcd-1b4f2ac29b9c/dqc_reference
[2024-01-25 19:01:21,911] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:21,911] [INFO] Task started: Prodigal
[2024-01-25 19:01:21,912] [INFO] Running command: gunzip -c /var/lib/cwl/stgf859ba33-5b6c-4b74-a555-bbb3b7b31bb3/GCF_024160185.1_ASM2416018v1_genomic.fna.gz | prodigal -d GCF_024160185.1_ASM2416018v1_genomic.fna/cds.fna -a GCF_024160185.1_ASM2416018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:28,001] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:28,001] [INFO] Task started: HMMsearch
[2024-01-25 19:01:28,001] [INFO] Running command: hmmsearch --tblout GCF_024160185.1_ASM2416018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64e17ee4-cf61-41ff-8dcd-1b4f2ac29b9c/dqc_reference/reference_markers.hmm GCF_024160185.1_ASM2416018v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:28,228] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:28,229] [INFO] Found 6/6 markers.
[2024-01-25 19:01:28,258] [INFO] Query marker FASTA was written to GCF_024160185.1_ASM2416018v1_genomic.fna/markers.fasta
[2024-01-25 19:01:28,258] [INFO] Task started: Blastn
[2024-01-25 19:01:28,258] [INFO] Running command: blastn -query GCF_024160185.1_ASM2416018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64e17ee4-cf61-41ff-8dcd-1b4f2ac29b9c/dqc_reference/reference_markers.fasta -out GCF_024160185.1_ASM2416018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:28,850] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:28,854] [INFO] Selected 23 target genomes.
[2024-01-25 19:01:28,854] [INFO] Target genome list was writen to GCF_024160185.1_ASM2416018v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:28,869] [INFO] Task started: fastANI
[2024-01-25 19:01:28,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgf859ba33-5b6c-4b74-a555-bbb3b7b31bb3/GCF_024160185.1_ASM2416018v1_genomic.fna.gz --refList GCF_024160185.1_ASM2416018v1_genomic.fna/target_genomes.txt --output GCF_024160185.1_ASM2416018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:42,062] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:42,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64e17ee4-cf61-41ff-8dcd-1b4f2ac29b9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:42,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64e17ee4-cf61-41ff-8dcd-1b4f2ac29b9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:42,068] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:01:42,068] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:42,068] [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
Ohessyouella blattaphilus	strain=PAL227	GCA_024721265.1	2949333	2949333	type	True	100.0	1033	1039	95	conclusive
Ohessyouella blattaphilus	strain=PAL227	GCA_024160185.1	2949333	2949333	type	True	100.0	1033	1039	95	conclusive
Aequitasia blattaphilus	strain=PAL113	GCA_024721305.1	2949332	2949332	type	True	81.8712	118	1039	95	below_threshold
Aequitasia blattaphilus	strain=PAL113	GCA_024160205.1	2949332	2949332	type	True	81.8712	118	1039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:42,069] [INFO] DFAST Taxonomy check result was written to GCF_024160185.1_ASM2416018v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:42,070] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:42,070] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:42,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64e17ee4-cf61-41ff-8dcd-1b4f2ac29b9c/dqc_reference/checkm_data
[2024-01-25 19:01:42,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:42,118] [INFO] Task started: CheckM
[2024-01-25 19:01:42,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024160185.1_ASM2416018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024160185.1_ASM2416018v1_genomic.fna/checkm_input GCF_024160185.1_ASM2416018v1_genomic.fna/checkm_result
[2024-01-25 19:02:05,165] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:05,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:05,210] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:05,211] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:05,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024160185.1_ASM2416018v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:05,212] [INFO] Task started: Blastn
[2024-01-25 19:02:05,212] [INFO] Running command: blastn -query GCF_024160185.1_ASM2416018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64e17ee4-cf61-41ff-8dcd-1b4f2ac29b9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024160185.1_ASM2416018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:06,261] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:06,265] [INFO] Selected 35 target genomes.
[2024-01-25 19:02:06,265] [INFO] Target genome list was writen to GCF_024160185.1_ASM2416018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:06,443] [INFO] Task started: fastANI
[2024-01-25 19:02:06,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgf859ba33-5b6c-4b74-a555-bbb3b7b31bb3/GCF_024160185.1_ASM2416018v1_genomic.fna.gz --refList GCF_024160185.1_ASM2416018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024160185.1_ASM2416018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:26,047] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:26,053] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:02:26,053] [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
--------------------------------------------------------------------------------
[2024-01-25 19:02:26,054] [INFO] GTDB search result was written to GCF_024160185.1_ASM2416018v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:26,055] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:26,057] [INFO] DFAST_QC result json was written to GCF_024160185.1_ASM2416018v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:26,058] [INFO] DFAST_QC completed!
[2024-01-25 19:02:26,058] [INFO] Total running time: 0h1m5s