[2023-06-16 23:30:19,488] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:30:19,491] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:30:19,491] [INFO] DQC Reference Directory: /var/lib/cwl/stgc24f4f74-279f-4361-bfd5-3e47e1f6013e/dqc_reference
[2023-06-16 23:30:21,164] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:30:21,164] [INFO] Task started: Prodigal
[2023-06-16 23:30:21,165] [INFO] Running command: gunzip -c /var/lib/cwl/stg90e912bf-eb3e-4a27-9bbb-912ed6863025/GCA_028821785.1_ASM2882178v1_genomic.fna.gz | prodigal -d GCA_028821785.1_ASM2882178v1_genomic.fna/cds.fna -a GCA_028821785.1_ASM2882178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:30:25,328] [INFO] Task succeeded: Prodigal
[2023-06-16 23:30:25,328] [INFO] Task started: HMMsearch
[2023-06-16 23:30:25,329] [INFO] Running command: hmmsearch --tblout GCA_028821785.1_ASM2882178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc24f4f74-279f-4361-bfd5-3e47e1f6013e/dqc_reference/reference_markers.hmm GCA_028821785.1_ASM2882178v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:30:25,559] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:30:25,562] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg90e912bf-eb3e-4a27-9bbb-912ed6863025/GCA_028821785.1_ASM2882178v1_genomic.fna.gz]
[2023-06-16 23:30:25,585] [INFO] Query marker FASTA was written to GCA_028821785.1_ASM2882178v1_genomic.fna/markers.fasta
[2023-06-16 23:30:25,585] [INFO] Task started: Blastn
[2023-06-16 23:30:25,585] [INFO] Running command: blastn -query GCA_028821785.1_ASM2882178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc24f4f74-279f-4361-bfd5-3e47e1f6013e/dqc_reference/reference_markers.fasta -out GCA_028821785.1_ASM2882178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:30:26,061] [INFO] Task succeeded: Blastn
[2023-06-16 23:30:26,066] [INFO] Selected 5 target genomes.
[2023-06-16 23:30:26,067] [INFO] Target genome list was writen to GCA_028821785.1_ASM2882178v1_genomic.fna/target_genomes.txt
[2023-06-16 23:30:26,069] [INFO] Task started: fastANI
[2023-06-16 23:30:26,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e912bf-eb3e-4a27-9bbb-912ed6863025/GCA_028821785.1_ASM2882178v1_genomic.fna.gz --refList GCA_028821785.1_ASM2882178v1_genomic.fna/target_genomes.txt --output GCA_028821785.1_ASM2882178v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:30:29,054] [INFO] Task succeeded: fastANI
[2023-06-16 23:30:29,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc24f4f74-279f-4361-bfd5-3e47e1f6013e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:30:29,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc24f4f74-279f-4361-bfd5-3e47e1f6013e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:30:29,058] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:30:29,058] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 23:30:29,058] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-16 23:30:29,060] [INFO] DFAST Taxonomy check result was written to GCA_028821785.1_ASM2882178v1_genomic.fna/tc_result.tsv
[2023-06-16 23:30:29,061] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:30:29,061] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:30:29,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc24f4f74-279f-4361-bfd5-3e47e1f6013e/dqc_reference/checkm_data
[2023-06-16 23:30:29,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:30:29,085] [INFO] Task started: CheckM
[2023-06-16 23:30:29,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028821785.1_ASM2882178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028821785.1_ASM2882178v1_genomic.fna/checkm_input GCA_028821785.1_ASM2882178v1_genomic.fna/checkm_result
[2023-06-16 23:30:49,042] [INFO] Task succeeded: CheckM
[2023-06-16 23:30:49,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 23:30:49,068] [INFO] ===== Completeness check finished =====
[2023-06-16 23:30:49,068] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:30:49,068] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028821785.1_ASM2882178v1_genomic.fna/markers.fasta)
[2023-06-16 23:30:49,069] [INFO] Task started: Blastn
[2023-06-16 23:30:49,069] [INFO] Running command: blastn -query GCA_028821785.1_ASM2882178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc24f4f74-279f-4361-bfd5-3e47e1f6013e/dqc_reference/reference_markers_gtdb.fasta -out GCA_028821785.1_ASM2882178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:30:49,542] [INFO] Task succeeded: Blastn
[2023-06-16 23:30:49,545] [INFO] Selected 8 target genomes.
[2023-06-16 23:30:49,546] [INFO] Target genome list was writen to GCA_028821785.1_ASM2882178v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:30:49,556] [INFO] Task started: fastANI
[2023-06-16 23:30:49,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e912bf-eb3e-4a27-9bbb-912ed6863025/GCA_028821785.1_ASM2882178v1_genomic.fna.gz --refList GCA_028821785.1_ASM2882178v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028821785.1_ASM2882178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:30:52,362] [INFO] Task succeeded: fastANI
[2023-06-16 23:30:52,371] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 23:30:52,371] [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_009937205.1	s__MGIIa-L1 sp009937205	93.4039	448	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002499015.1	s__MGIIa-L1 sp002499015	92.6908	472	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182185.1	s__MGIIa-L1 sp905182185	90.2972	392	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650105.1	s__MGIIa-L1 sp018650105	80.3214	306	564	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.04	99.04	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-16 23:30:52,373] [INFO] GTDB search result was written to GCA_028821785.1_ASM2882178v1_genomic.fna/result_gtdb.tsv
[2023-06-16 23:30:52,374] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:30:52,377] [INFO] DFAST_QC result json was written to GCA_028821785.1_ASM2882178v1_genomic.fna/dqc_result.json
[2023-06-16 23:30:52,377] [INFO] DFAST_QC completed!
[2023-06-16 23:30:52,377] [INFO] Total running time: 0h0m33s