[2024-01-24 12:36:24,874] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,876] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,876] [INFO] DQC Reference Directory: /var/lib/cwl/stga5cee8cf-ddb4-4c62-bc58-78bb3d8fb855/dqc_reference
[2024-01-24 12:36:26,225] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,225] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,226] [INFO] Running command: gunzip -c /var/lib/cwl/stgebb6c4c7-12f2-4eeb-83cb-6f0a2caa901f/GCF_019175345.1_ASM1917534v1_genomic.fna.gz | prodigal -d GCF_019175345.1_ASM1917534v1_genomic.fna/cds.fna -a GCF_019175345.1_ASM1917534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:35,132] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:35,132] [INFO] Task started: HMMsearch
[2024-01-24 12:36:35,132] [INFO] Running command: hmmsearch --tblout GCF_019175345.1_ASM1917534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5cee8cf-ddb4-4c62-bc58-78bb3d8fb855/dqc_reference/reference_markers.hmm GCF_019175345.1_ASM1917534v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:35,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:35,371] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgebb6c4c7-12f2-4eeb-83cb-6f0a2caa901f/GCF_019175345.1_ASM1917534v1_genomic.fna.gz]
[2024-01-24 12:36:35,397] [INFO] Query marker FASTA was written to GCF_019175345.1_ASM1917534v1_genomic.fna/markers.fasta
[2024-01-24 12:36:35,397] [INFO] Task started: Blastn
[2024-01-24 12:36:35,398] [INFO] Running command: blastn -query GCF_019175345.1_ASM1917534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5cee8cf-ddb4-4c62-bc58-78bb3d8fb855/dqc_reference/reference_markers.fasta -out GCF_019175345.1_ASM1917534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:35,910] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:35,914] [INFO] Selected 0 target genomes.
[2024-01-24 12:36:35,914] [INFO] Target genome list was writen to GCF_019175345.1_ASM1917534v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:35,915] [ERROR] File is empty. [GCF_019175345.1_ASM1917534v1_genomic.fna/target_genomes.txt]
[2024-01-24 12:36:35,915] [ERROR] Task failed. No target genome found.
[2024-01-24 12:36:35,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:35,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5cee8cf-ddb4-4c62-bc58-78bb3d8fb855/dqc_reference/checkm_data
[2024-01-24 12:36:35,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:35,948] [INFO] Task started: CheckM
[2024-01-24 12:36:35,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019175345.1_ASM1917534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019175345.1_ASM1917534v1_genomic.fna/checkm_input GCF_019175345.1_ASM1917534v1_genomic.fna/checkm_result
[2024-01-24 12:37:06,472] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:06,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:06,495] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:06,496] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:06,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019175345.1_ASM1917534v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:06,497] [INFO] Task started: Blastn
[2024-01-24 12:37:06,497] [INFO] Running command: blastn -query GCF_019175345.1_ASM1917534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5cee8cf-ddb4-4c62-bc58-78bb3d8fb855/dqc_reference/reference_markers_gtdb.fasta -out GCF_019175345.1_ASM1917534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:06,941] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:06,950] [INFO] Selected 5 target genomes.
[2024-01-24 12:37:06,950] [INFO] Target genome list was writen to GCF_019175345.1_ASM1917534v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:06,957] [INFO] Task started: fastANI
[2024-01-24 12:37:06,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb6c4c7-12f2-4eeb-83cb-6f0a2caa901f/GCF_019175345.1_ASM1917534v1_genomic.fna.gz --refList GCF_019175345.1_ASM1917534v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019175345.1_ASM1917534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:11,027] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:11,033] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:11,033] [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_019175345.1	s__Saccharolobus shibatae	100.0	966	971	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus	95.0	98.28	98.16	0.87	0.86	3	conclusive
GCF_000022485.1	s__Saccharolobus islandicus	93.8491	756	971	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus	95.0	98.20	97.71	0.90	0.87	24	-
GCF_009601705.1	s__Saccharolobus sp009601705	87.7362	682	971	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus	95.0	99.16	99.16	0.85	0.85	2	-
GCF_900079115.1	s__Saccharolobus solfataricus	87.2951	710	971	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus	95.0	99.10	99.01	0.93	0.91	15	-
GCF_001719125.1	s__Saccharolobus sp001719125	76.8066	146	971	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus	95.0	99.96	99.93	0.99	0.97	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:11,034] [INFO] GTDB search result was written to GCF_019175345.1_ASM1917534v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:11,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:11,037] [INFO] DFAST_QC result json was written to GCF_019175345.1_ASM1917534v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:11,037] [INFO] DFAST_QC completed!
[2024-01-24 12:37:11,037] [INFO] Total running time: 0h0m46s