[2024-01-24 10:47:24,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg5165bc96-4e7c-4d68-80f2-aec933d2878e/dqc_reference
[2024-01-24 10:47:26,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,400] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,400] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7edd4c7-9bc8-46ef-ac88-5d412e4bd432/GCF_900079115.1_SSOP1_genomic.fna.gz | prodigal -d GCF_900079115.1_SSOP1_genomic.fna/cds.fna -a GCF_900079115.1_SSOP1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:35,728] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:35,729] [INFO] Task started: HMMsearch
[2024-01-24 10:47:35,729] [INFO] Running command: hmmsearch --tblout GCF_900079115.1_SSOP1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5165bc96-4e7c-4d68-80f2-aec933d2878e/dqc_reference/reference_markers.hmm GCF_900079115.1_SSOP1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:35,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:35,992] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgc7edd4c7-9bc8-46ef-ac88-5d412e4bd432/GCF_900079115.1_SSOP1_genomic.fna.gz]
[2024-01-24 10:47:36,018] [INFO] Query marker FASTA was written to GCF_900079115.1_SSOP1_genomic.fna/markers.fasta
[2024-01-24 10:47:36,019] [INFO] Task started: Blastn
[2024-01-24 10:47:36,019] [INFO] Running command: blastn -query GCF_900079115.1_SSOP1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5165bc96-4e7c-4d68-80f2-aec933d2878e/dqc_reference/reference_markers.fasta -out GCF_900079115.1_SSOP1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:36,539] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:36,546] [INFO] Selected 0 target genomes.
[2024-01-24 10:47:36,546] [INFO] Target genome list was writen to GCF_900079115.1_SSOP1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:36,547] [ERROR] File is empty. [GCF_900079115.1_SSOP1_genomic.fna/target_genomes.txt]
[2024-01-24 10:47:36,547] [ERROR] Task failed. No target genome found.
[2024-01-24 10:47:36,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:36,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5165bc96-4e7c-4d68-80f2-aec933d2878e/dqc_reference/checkm_data
[2024-01-24 10:47:36,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:36,587] [INFO] Task started: CheckM
[2024-01-24 10:47:36,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900079115.1_SSOP1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900079115.1_SSOP1_genomic.fna/checkm_input GCF_900079115.1_SSOP1_genomic.fna/checkm_result
[2024-01-24 10:48:07,883] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:07,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:07,906] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:07,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:07,907] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900079115.1_SSOP1_genomic.fna/markers.fasta)
[2024-01-24 10:48:07,908] [INFO] Task started: Blastn
[2024-01-24 10:48:07,908] [INFO] Running command: blastn -query GCF_900079115.1_SSOP1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5165bc96-4e7c-4d68-80f2-aec933d2878e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900079115.1_SSOP1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:08,392] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:08,397] [INFO] Selected 5 target genomes.
[2024-01-24 10:48:08,397] [INFO] Target genome list was writen to GCF_900079115.1_SSOP1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:08,403] [INFO] Task started: fastANI
[2024-01-24 10:48:08,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7edd4c7-9bc8-46ef-ac88-5d412e4bd432/GCF_900079115.1_SSOP1_genomic.fna.gz --refList GCF_900079115.1_SSOP1_genomic.fna/target_genomes_gtdb.txt --output GCF_900079115.1_SSOP1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:14,285] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:14,294] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:14,294] [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_900079115.1	s__Saccharolobus solfataricus	100.0	1011	1011	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus	95.0	99.10	99.01	0.93	0.91	15	conclusive
GCF_000022485.1	s__Saccharolobus islandicus	88.2179	715	1011	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus	95.0	98.20	97.71	0.90	0.87	24	-
GCF_019175345.1	s__Saccharolobus shibatae	87.1678	731	1011	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus	95.0	98.28	98.16	0.87	0.86	3	-
GCF_009601705.1	s__Saccharolobus sp009601705	85.7332	676	1011	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Saccharolobus	95.0	99.16	99.16	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:14,295] [INFO] GTDB search result was written to GCF_900079115.1_SSOP1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:14,296] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:14,298] [INFO] DFAST_QC result json was written to GCF_900079115.1_SSOP1_genomic.fna/dqc_result.json
[2024-01-24 10:48:14,298] [INFO] DFAST_QC completed!
[2024-01-24 10:48:14,298] [INFO] Total running time: 0h0m50s