[2023-06-30 06:33:27,647] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:33:27,649] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:33:27,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg79525b50-0440-42ec-9381-7e876e6938cf/dqc_reference
[2023-06-30 06:33:28,989] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:33:28,990] [INFO] Task started: Prodigal
[2023-06-30 06:33:28,990] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c3dbcfc-a9c4-4c40-a493-19a29e2a24c8/GCA_024707015.1_ASM2470701v1_genomic.fna.gz | prodigal -d GCA_024707015.1_ASM2470701v1_genomic.fna/cds.fna -a GCA_024707015.1_ASM2470701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:33:32,847] [INFO] Task succeeded: Prodigal
[2023-06-30 06:33:32,847] [INFO] Task started: HMMsearch
[2023-06-30 06:33:32,848] [INFO] Running command: hmmsearch --tblout GCA_024707015.1_ASM2470701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79525b50-0440-42ec-9381-7e876e6938cf/dqc_reference/reference_markers.hmm GCA_024707015.1_ASM2470701v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:33:32,993] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:33:32,994] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9c3dbcfc-a9c4-4c40-a493-19a29e2a24c8/GCA_024707015.1_ASM2470701v1_genomic.fna.gz]
[2023-06-30 06:33:33,013] [INFO] Query marker FASTA was written to GCA_024707015.1_ASM2470701v1_genomic.fna/markers.fasta
[2023-06-30 06:33:33,014] [INFO] Task started: Blastn
[2023-06-30 06:33:33,014] [INFO] Running command: blastn -query GCA_024707015.1_ASM2470701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79525b50-0440-42ec-9381-7e876e6938cf/dqc_reference/reference_markers.fasta -out GCA_024707015.1_ASM2470701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:33:33,493] [INFO] Task succeeded: Blastn
[2023-06-30 06:33:33,496] [INFO] Selected 0 target genomes.
[2023-06-30 06:33:33,497] [INFO] Target genome list was writen to GCA_024707015.1_ASM2470701v1_genomic.fna/target_genomes.txt
[2023-06-30 06:33:33,497] [ERROR] File is empty. [GCA_024707015.1_ASM2470701v1_genomic.fna/target_genomes.txt]
[2023-06-30 06:33:33,497] [ERROR] Task failed. No target genome found.
[2023-06-30 06:33:33,497] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:33:33,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79525b50-0440-42ec-9381-7e876e6938cf/dqc_reference/checkm_data
[2023-06-30 06:33:33,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:33:33,519] [INFO] Task started: CheckM
[2023-06-30 06:33:33,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024707015.1_ASM2470701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024707015.1_ASM2470701v1_genomic.fna/checkm_input GCA_024707015.1_ASM2470701v1_genomic.fna/checkm_result
[2023-06-30 06:33:53,859] [INFO] Task succeeded: CheckM
[2023-06-30 06:33:53,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:33:53,883] [INFO] ===== Completeness check finished =====
[2023-06-30 06:33:53,883] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:33:53,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024707015.1_ASM2470701v1_genomic.fna/markers.fasta)
[2023-06-30 06:33:53,883] [INFO] Task started: Blastn
[2023-06-30 06:33:53,884] [INFO] Running command: blastn -query GCA_024707015.1_ASM2470701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79525b50-0440-42ec-9381-7e876e6938cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_024707015.1_ASM2470701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:33:54,438] [INFO] Task succeeded: Blastn
[2023-06-30 06:33:54,441] [INFO] Selected 3 target genomes.
[2023-06-30 06:33:54,442] [INFO] Target genome list was writen to GCA_024707015.1_ASM2470701v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:33:54,445] [INFO] Task started: fastANI
[2023-06-30 06:33:54,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c3dbcfc-a9c4-4c40-a493-19a29e2a24c8/GCA_024707015.1_ASM2470701v1_genomic.fna.gz --refList GCA_024707015.1_ASM2470701v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024707015.1_ASM2470701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:33:55,173] [INFO] Task succeeded: fastANI
[2023-06-30 06:33:55,177] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 06:33:55,178] [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_011605825.1	s__DSZF01 sp011605825	99.1678	96	549	d__Archaea;p__Thermoproteota;c__Methanomethylicia;o__B29-G17;f__DSZF01;g__DSZF01	95.0	99.47	99.47	0.51	0.51	2	conclusive
GCA_011372955.1	s__DSZF01 sp011372955	86.0663	369	549	d__Archaea;p__Thermoproteota;c__Methanomethylicia;o__B29-G17;f__DSZF01;g__DSZF01	95.0	99.38	99.38	0.76	0.76	2	-
GCA_011367155.1	s__DSZF01 sp011367155	77.2597	85	549	d__Archaea;p__Thermoproteota;c__Methanomethylicia;o__B29-G17;f__DSZF01;g__DSZF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:33:55,180] [INFO] GTDB search result was written to GCA_024707015.1_ASM2470701v1_genomic.fna/result_gtdb.tsv
[2023-06-30 06:33:55,180] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:33:55,182] [INFO] DFAST_QC result json was written to GCA_024707015.1_ASM2470701v1_genomic.fna/dqc_result.json
[2023-06-30 06:33:55,182] [INFO] DFAST_QC completed!
[2023-06-30 06:33:55,183] [INFO] Total running time: 0h0m28s