[2023-06-27 05:57:51,686] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:57:51,689] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:57:51,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2eadd10-1b0c-41d5-8a63-8c1026c1a5e8/dqc_reference
[2023-06-27 05:57:53,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:57:53,073] [INFO] Task started: Prodigal
[2023-06-27 05:57:53,073] [INFO] Running command: gunzip -c /var/lib/cwl/stgd13ea08e-e26b-4d89-ba4b-7ed2f9807806/GCA_002683155.1_ASM268315v1_genomic.fna.gz | prodigal -d GCA_002683155.1_ASM268315v1_genomic.fna/cds.fna -a GCA_002683155.1_ASM268315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:57:55,116] [INFO] Task succeeded: Prodigal
[2023-06-27 05:57:55,116] [INFO] Task started: HMMsearch
[2023-06-27 05:57:55,116] [INFO] Running command: hmmsearch --tblout GCA_002683155.1_ASM268315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2eadd10-1b0c-41d5-8a63-8c1026c1a5e8/dqc_reference/reference_markers.hmm GCA_002683155.1_ASM268315v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:57:55,320] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:57:55,322] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgd13ea08e-e26b-4d89-ba4b-7ed2f9807806/GCA_002683155.1_ASM268315v1_genomic.fna.gz]
[2023-06-27 05:57:55,349] [INFO] Query marker FASTA was written to GCA_002683155.1_ASM268315v1_genomic.fna/markers.fasta
[2023-06-27 05:57:55,349] [INFO] Task started: Blastn
[2023-06-27 05:57:55,350] [INFO] Running command: blastn -query GCA_002683155.1_ASM268315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2eadd10-1b0c-41d5-8a63-8c1026c1a5e8/dqc_reference/reference_markers.fasta -out GCA_002683155.1_ASM268315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:57:55,847] [INFO] Task succeeded: Blastn
[2023-06-27 05:57:55,851] [INFO] Selected 0 target genomes.
[2023-06-27 05:57:55,852] [INFO] Target genome list was writen to GCA_002683155.1_ASM268315v1_genomic.fna/target_genomes.txt
[2023-06-27 05:57:55,852] [ERROR] File is empty. [GCA_002683155.1_ASM268315v1_genomic.fna/target_genomes.txt]
[2023-06-27 05:57:55,852] [ERROR] Task failed. No target genome found.
[2023-06-27 05:57:55,853] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:57:55,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2eadd10-1b0c-41d5-8a63-8c1026c1a5e8/dqc_reference/checkm_data
[2023-06-27 05:57:55,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:57:55,874] [INFO] Task started: CheckM
[2023-06-27 05:57:55,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002683155.1_ASM268315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002683155.1_ASM268315v1_genomic.fna/checkm_input GCA_002683155.1_ASM268315v1_genomic.fna/checkm_result
[2023-06-27 05:58:13,640] [INFO] Task succeeded: CheckM
[2023-06-27 05:58:13,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:58:13,660] [INFO] ===== Completeness check finished =====
[2023-06-27 05:58:13,660] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:58:13,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002683155.1_ASM268315v1_genomic.fna/markers.fasta)
[2023-06-27 05:58:13,661] [INFO] Task started: Blastn
[2023-06-27 05:58:13,661] [INFO] Running command: blastn -query GCA_002683155.1_ASM268315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2eadd10-1b0c-41d5-8a63-8c1026c1a5e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_002683155.1_ASM268315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:58:14,297] [INFO] Task succeeded: Blastn
[2023-06-27 05:58:14,302] [INFO] Selected 6 target genomes.
[2023-06-27 05:58:14,302] [INFO] Target genome list was writen to GCA_002683155.1_ASM268315v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:58:14,307] [INFO] Task started: fastANI
[2023-06-27 05:58:14,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgd13ea08e-e26b-4d89-ba4b-7ed2f9807806/GCA_002683155.1_ASM268315v1_genomic.fna.gz --refList GCA_002683155.1_ASM268315v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002683155.1_ASM268315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:58:15,719] [INFO] Task succeeded: fastANI
[2023-06-27 05:58:15,728] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:58:15,729] [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_002683155.1	s__MGIIb-O3 sp002683155	100.0	256	258	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014239955.1	s__MGIIb-O3 sp014239955	78.6799	138	258	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902573015.1	s__MGIIb-O3 sp902573015	77.5307	51	258	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:58:15,735] [INFO] GTDB search result was written to GCA_002683155.1_ASM268315v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:58:15,736] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:58:15,739] [INFO] DFAST_QC result json was written to GCA_002683155.1_ASM268315v1_genomic.fna/dqc_result.json
[2023-06-27 05:58:15,740] [INFO] DFAST_QC completed!
[2023-06-27 05:58:15,740] [INFO] Total running time: 0h0m24s