[2023-06-07 22:55:03,505] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:55:03,508] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:55:03,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg02cb3479-0fd3-4c84-aaeb-85e44b67fa07/dqc_reference
[2023-06-07 22:55:04,808] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:55:04,810] [INFO] Task started: Prodigal
[2023-06-07 22:55:04,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg16133305-279c-4e36-82db-a56cffffd07b/GCA_902826075.1_RBC071_genomic.fna.gz | prodigal -d GCA_902826075.1_RBC071_genomic.fna/cds.fna -a GCA_902826075.1_RBC071_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:55:13,083] [INFO] Task succeeded: Prodigal
[2023-06-07 22:55:13,084] [INFO] Task started: HMMsearch
[2023-06-07 22:55:13,084] [INFO] Running command: hmmsearch --tblout GCA_902826075.1_RBC071_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02cb3479-0fd3-4c84-aaeb-85e44b67fa07/dqc_reference/reference_markers.hmm GCA_902826075.1_RBC071_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:55:13,304] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:55:13,305] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg16133305-279c-4e36-82db-a56cffffd07b/GCA_902826075.1_RBC071_genomic.fna.gz]
[2023-06-07 22:55:13,342] [INFO] Query marker FASTA was written to GCA_902826075.1_RBC071_genomic.fna/markers.fasta
[2023-06-07 22:55:13,343] [INFO] Task started: Blastn
[2023-06-07 22:55:13,343] [INFO] Running command: blastn -query GCA_902826075.1_RBC071_genomic.fna/markers.fasta -db /var/lib/cwl/stg02cb3479-0fd3-4c84-aaeb-85e44b67fa07/dqc_reference/reference_markers.fasta -out GCA_902826075.1_RBC071_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:13,814] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:13,818] [INFO] Selected 0 target genomes.
[2023-06-07 22:55:13,818] [INFO] Target genome list was writen to GCA_902826075.1_RBC071_genomic.fna/target_genomes.txt
[2023-06-07 22:55:13,818] [ERROR] File is empty. [GCA_902826075.1_RBC071_genomic.fna/target_genomes.txt]
[2023-06-07 22:55:13,818] [ERROR] Task failed. No target genome found.
[2023-06-07 22:55:13,818] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:55:13,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02cb3479-0fd3-4c84-aaeb-85e44b67fa07/dqc_reference/checkm_data
[2023-06-07 22:55:13,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:55:13,852] [INFO] Task started: CheckM
[2023-06-07 22:55:13,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902826075.1_RBC071_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902826075.1_RBC071_genomic.fna/checkm_input GCA_902826075.1_RBC071_genomic.fna/checkm_result
[2023-06-07 22:55:43,873] [INFO] Task succeeded: CheckM
[2023-06-07 22:55:43,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:55:43,897] [INFO] ===== Completeness check finished =====
[2023-06-07 22:55:43,897] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:55:43,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902826075.1_RBC071_genomic.fna/markers.fasta)
[2023-06-07 22:55:43,898] [INFO] Task started: Blastn
[2023-06-07 22:55:43,898] [INFO] Running command: blastn -query GCA_902826075.1_RBC071_genomic.fna/markers.fasta -db /var/lib/cwl/stg02cb3479-0fd3-4c84-aaeb-85e44b67fa07/dqc_reference/reference_markers_gtdb.fasta -out GCA_902826075.1_RBC071_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:44,373] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:44,378] [INFO] Selected 5 target genomes.
[2023-06-07 22:55:44,378] [INFO] Target genome list was writen to GCA_902826075.1_RBC071_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:55:44,506] [INFO] Task started: fastANI
[2023-06-07 22:55:44,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg16133305-279c-4e36-82db-a56cffffd07b/GCA_902826075.1_RBC071_genomic.fna.gz --refList GCA_902826075.1_RBC071_genomic.fna/target_genomes_gtdb.txt --output GCA_902826075.1_RBC071_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:55:46,805] [INFO] Task succeeded: fastANI
[2023-06-07 22:55:46,813] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:55:46,814] [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
GCF_001870125.1	s__Nitrosocosmicus hydrocola	96.0893	655	755	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrososphaeraceae;g__Nitrosocosmicus	95.0	96.12	96.12	0.87	0.87	2	conclusive
GCA_013114705.1	s__Nitrosocosmicus sp013114705	83.3413	411	755	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrososphaeraceae;g__Nitrosocosmicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008389435.1	s__Nitrosocosmicus sp008389435	78.2796	176	755	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrososphaeraceae;g__Nitrosocosmicus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-07 22:55:46,816] [INFO] GTDB search result was written to GCA_902826075.1_RBC071_genomic.fna/result_gtdb.tsv
[2023-06-07 22:55:46,817] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:55:46,820] [INFO] DFAST_QC result json was written to GCA_902826075.1_RBC071_genomic.fna/dqc_result.json
[2023-06-07 22:55:46,820] [INFO] DFAST_QC completed!
[2023-06-07 22:55:46,820] [INFO] Total running time: 0h0m43s