[2023-06-19 08:43:30,003] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:43:30,005] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:43:30,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg347b9282-8667-480d-8a16-eccd2076e602/dqc_reference
[2023-06-19 08:43:31,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:43:31,381] [INFO] Task started: Prodigal
[2023-06-19 08:43:31,381] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb155acb-3c0c-48e9-9f4f-fe86683cb76b/GCA_018660715.1_ASM1866071v1_genomic.fna.gz | prodigal -d GCA_018660715.1_ASM1866071v1_genomic.fna/cds.fna -a GCA_018660715.1_ASM1866071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:43:37,112] [INFO] Task succeeded: Prodigal
[2023-06-19 08:43:37,113] [INFO] Task started: HMMsearch
[2023-06-19 08:43:37,113] [INFO] Running command: hmmsearch --tblout GCA_018660715.1_ASM1866071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg347b9282-8667-480d-8a16-eccd2076e602/dqc_reference/reference_markers.hmm GCA_018660715.1_ASM1866071v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:43:37,380] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:43:37,382] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfb155acb-3c0c-48e9-9f4f-fe86683cb76b/GCA_018660715.1_ASM1866071v1_genomic.fna.gz]
[2023-06-19 08:43:37,413] [INFO] Query marker FASTA was written to GCA_018660715.1_ASM1866071v1_genomic.fna/markers.fasta
[2023-06-19 08:43:37,413] [INFO] Task started: Blastn
[2023-06-19 08:43:37,414] [INFO] Running command: blastn -query GCA_018660715.1_ASM1866071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg347b9282-8667-480d-8a16-eccd2076e602/dqc_reference/reference_markers.fasta -out GCA_018660715.1_ASM1866071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:43:37,902] [INFO] Task succeeded: Blastn
[2023-06-19 08:43:37,908] [INFO] Selected 5 target genomes.
[2023-06-19 08:43:37,909] [INFO] Target genome list was writen to GCA_018660715.1_ASM1866071v1_genomic.fna/target_genomes.txt
[2023-06-19 08:43:37,911] [INFO] Task started: fastANI
[2023-06-19 08:43:37,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb155acb-3c0c-48e9-9f4f-fe86683cb76b/GCA_018660715.1_ASM1866071v1_genomic.fna.gz --refList GCA_018660715.1_ASM1866071v1_genomic.fna/target_genomes.txt --output GCA_018660715.1_ASM1866071v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:43:41,782] [INFO] Task succeeded: fastANI
[2023-06-19 08:43:41,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg347b9282-8667-480d-8a16-eccd2076e602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:43:41,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg347b9282-8667-480d-8a16-eccd2076e602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:43:41,785] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:43:41,786] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:43:41,786] [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
--------------------------------------------------------------------------------
[2023-06-19 08:43:41,788] [INFO] DFAST Taxonomy check result was written to GCA_018660715.1_ASM1866071v1_genomic.fna/tc_result.tsv
[2023-06-19 08:43:41,789] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:43:41,789] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:43:41,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg347b9282-8667-480d-8a16-eccd2076e602/dqc_reference/checkm_data
[2023-06-19 08:43:41,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:43:41,818] [INFO] Task started: CheckM
[2023-06-19 08:43:41,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018660715.1_ASM1866071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018660715.1_ASM1866071v1_genomic.fna/checkm_input GCA_018660715.1_ASM1866071v1_genomic.fna/checkm_result
[2023-06-19 08:44:06,998] [INFO] Task succeeded: CheckM
[2023-06-19 08:44:07,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:44:07,019] [INFO] ===== Completeness check finished =====
[2023-06-19 08:44:07,020] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:44:07,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018660715.1_ASM1866071v1_genomic.fna/markers.fasta)
[2023-06-19 08:44:07,020] [INFO] Task started: Blastn
[2023-06-19 08:44:07,021] [INFO] Running command: blastn -query GCA_018660715.1_ASM1866071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg347b9282-8667-480d-8a16-eccd2076e602/dqc_reference/reference_markers_gtdb.fasta -out GCA_018660715.1_ASM1866071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:44:07,486] [INFO] Task succeeded: Blastn
[2023-06-19 08:44:07,490] [INFO] Selected 9 target genomes.
[2023-06-19 08:44:07,491] [INFO] Target genome list was writen to GCA_018660715.1_ASM1866071v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:44:07,500] [INFO] Task started: fastANI
[2023-06-19 08:44:07,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb155acb-3c0c-48e9-9f4f-fe86683cb76b/GCA_018660715.1_ASM1866071v1_genomic.fna.gz --refList GCA_018660715.1_ASM1866071v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018660715.1_ASM1866071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:44:10,616] [INFO] Task succeeded: fastANI
[2023-06-19 08:44:10,624] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:44:10,625] [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_000246735.1	s__MGIIa-L1 sp000246735	99.3193	438	494	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.40	99.32	0.97	0.89	6	conclusive
GCA_009887095.1	s__MGIIa-L1 sp009887095	87.9046	335	494	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_013330285.1	s__MGIIa-L1 sp8160u	79.4894	183	494	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	97.88	96.83	0.79	0.69	4	-
GCA_013329255.1	s__MGIIa-L1 sp9513u	79.4367	188	494	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_002502605.1	s__MGIIa-L1 sp002502605	79.111	192	494	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.35	99.06	0.87	0.87	3	-
GCA_905181785.1	s__MGIIa-L1 sp905181785	78.9399	173	494	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_003602645.1	s__MGIIa-L1 sp003602645	78.3997	177	494	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_003602475.1	s__Poseidonia sp003602475	77.3486	51	494	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	95.17	95.17	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-19 08:44:10,627] [INFO] GTDB search result was written to GCA_018660715.1_ASM1866071v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:44:10,627] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:44:10,631] [INFO] DFAST_QC result json was written to GCA_018660715.1_ASM1866071v1_genomic.fna/dqc_result.json
[2023-06-19 08:44:10,631] [INFO] DFAST_QC completed!
[2023-06-19 08:44:10,632] [INFO] Total running time: 0h0m41s