[2023-06-29 18:37:36,250] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:37:36,252] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:37:36,252] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a397c8c-b103-4f09-96b8-43931d0c20ae/dqc_reference
[2023-06-29 18:37:37,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:37:37,582] [INFO] Task started: Prodigal
[2023-06-29 18:37:37,582] [INFO] Running command: gunzip -c /var/lib/cwl/stg25e91883-9039-43c0-8ce3-6b50f823feda/GCA_011043475.1_ASM1104347v1_genomic.fna.gz | prodigal -d GCA_011043475.1_ASM1104347v1_genomic.fna/cds.fna -a GCA_011043475.1_ASM1104347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:37:40,767] [INFO] Task succeeded: Prodigal
[2023-06-29 18:37:40,768] [INFO] Task started: HMMsearch
[2023-06-29 18:37:40,768] [INFO] Running command: hmmsearch --tblout GCA_011043475.1_ASM1104347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a397c8c-b103-4f09-96b8-43931d0c20ae/dqc_reference/reference_markers.hmm GCA_011043475.1_ASM1104347v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:37:40,971] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:37:40,973] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg25e91883-9039-43c0-8ce3-6b50f823feda/GCA_011043475.1_ASM1104347v1_genomic.fna.gz]
[2023-06-29 18:37:40,994] [INFO] Query marker FASTA was written to GCA_011043475.1_ASM1104347v1_genomic.fna/markers.fasta
[2023-06-29 18:37:40,994] [INFO] Task started: Blastn
[2023-06-29 18:37:40,994] [INFO] Running command: blastn -query GCA_011043475.1_ASM1104347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a397c8c-b103-4f09-96b8-43931d0c20ae/dqc_reference/reference_markers.fasta -out GCA_011043475.1_ASM1104347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:37:41,490] [INFO] Task succeeded: Blastn
[2023-06-29 18:37:41,494] [INFO] Selected 0 target genomes.
[2023-06-29 18:37:41,494] [INFO] Target genome list was writen to GCA_011043475.1_ASM1104347v1_genomic.fna/target_genomes.txt
[2023-06-29 18:37:41,494] [ERROR] File is empty. [GCA_011043475.1_ASM1104347v1_genomic.fna/target_genomes.txt]
[2023-06-29 18:37:41,494] [ERROR] Task failed. No target genome found.
[2023-06-29 18:37:41,494] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:37:41,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a397c8c-b103-4f09-96b8-43931d0c20ae/dqc_reference/checkm_data
[2023-06-29 18:37:41,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:37:41,520] [INFO] Task started: CheckM
[2023-06-29 18:37:41,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011043475.1_ASM1104347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011043475.1_ASM1104347v1_genomic.fna/checkm_input GCA_011043475.1_ASM1104347v1_genomic.fna/checkm_result
[2023-06-29 18:37:59,574] [INFO] Task succeeded: CheckM
[2023-06-29 18:37:59,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.88%
Contamintation: 0.90%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 18:37:59,603] [INFO] ===== Completeness check finished =====
[2023-06-29 18:37:59,604] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:37:59,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011043475.1_ASM1104347v1_genomic.fna/markers.fasta)
[2023-06-29 18:37:59,604] [INFO] Task started: Blastn
[2023-06-29 18:37:59,604] [INFO] Running command: blastn -query GCA_011043475.1_ASM1104347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a397c8c-b103-4f09-96b8-43931d0c20ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_011043475.1_ASM1104347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:38:00,050] [INFO] Task succeeded: Blastn
[2023-06-29 18:38:00,055] [INFO] Selected 5 target genomes.
[2023-06-29 18:38:00,055] [INFO] Target genome list was writen to GCA_011043475.1_ASM1104347v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:38:00,059] [INFO] Task started: fastANI
[2023-06-29 18:38:00,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e91883-9039-43c0-8ce3-6b50f823feda/GCA_011043475.1_ASM1104347v1_genomic.fna.gz --refList GCA_011043475.1_ASM1104347v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011043475.1_ASM1104347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:38:02,519] [INFO] Task succeeded: fastANI
[2023-06-29 18:38:02,524] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 18:38:02,524] [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_003661105.1	s__Methanogaster sp003661105	97.9867	239	327	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanogasteraceae;g__Methanogaster	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003194445.1	s__Methanogaster sp003194445	91.1729	250	327	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanogasteraceae;g__Methanogaster	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013572355.1	s__Methanogaster sp013572355	88.6227	198	327	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanogasteraceae;g__Methanogaster	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003601535.1	s__Methanogaster sp003601535	79.0272	110	327	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanogasteraceae;g__Methanogaster	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 18:38:02,526] [INFO] GTDB search result was written to GCA_011043475.1_ASM1104347v1_genomic.fna/result_gtdb.tsv
[2023-06-29 18:38:02,527] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:38:02,531] [INFO] DFAST_QC result json was written to GCA_011043475.1_ASM1104347v1_genomic.fna/dqc_result.json
[2023-06-29 18:38:02,531] [INFO] DFAST_QC completed!
[2023-06-29 18:38:02,531] [INFO] Total running time: 0h0m26s