[2023-06-13 14:34:11,571] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:34:11,575] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:34:11,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg520688a3-681f-45ad-890c-3a2d8d57de21/dqc_reference
[2023-06-13 14:34:12,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:34:12,938] [INFO] Task started: Prodigal
[2023-06-13 14:34:12,939] [INFO] Running command: gunzip -c /var/lib/cwl/stga3ec23e5-de21-4aec-8a26-525f77addb7e/GCA_022769885.1_ASM2276988v1_genomic.fna.gz | prodigal -d GCA_022769885.1_ASM2276988v1_genomic.fna/cds.fna -a GCA_022769885.1_ASM2276988v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:34:22,084] [INFO] Task succeeded: Prodigal
[2023-06-13 14:34:22,084] [INFO] Task started: HMMsearch
[2023-06-13 14:34:22,084] [INFO] Running command: hmmsearch --tblout GCA_022769885.1_ASM2276988v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg520688a3-681f-45ad-890c-3a2d8d57de21/dqc_reference/reference_markers.hmm GCA_022769885.1_ASM2276988v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:34:22,282] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:34:22,283] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga3ec23e5-de21-4aec-8a26-525f77addb7e/GCA_022769885.1_ASM2276988v1_genomic.fna.gz]
[2023-06-13 14:34:22,317] [INFO] Query marker FASTA was written to GCA_022769885.1_ASM2276988v1_genomic.fna/markers.fasta
[2023-06-13 14:34:22,318] [INFO] Task started: Blastn
[2023-06-13 14:34:22,318] [INFO] Running command: blastn -query GCA_022769885.1_ASM2276988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg520688a3-681f-45ad-890c-3a2d8d57de21/dqc_reference/reference_markers.fasta -out GCA_022769885.1_ASM2276988v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:34:22,826] [INFO] Task succeeded: Blastn
[2023-06-13 14:34:22,830] [INFO] Selected 8 target genomes.
[2023-06-13 14:34:22,830] [INFO] Target genome list was writen to GCA_022769885.1_ASM2276988v1_genomic.fna/target_genomes.txt
[2023-06-13 14:34:22,831] [INFO] Task started: fastANI
[2023-06-13 14:34:22,831] [INFO] Running command: fastANI --query /var/lib/cwl/stga3ec23e5-de21-4aec-8a26-525f77addb7e/GCA_022769885.1_ASM2276988v1_genomic.fna.gz --refList GCA_022769885.1_ASM2276988v1_genomic.fna/target_genomes.txt --output GCA_022769885.1_ASM2276988v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:34:27,239] [INFO] Task succeeded: fastANI
[2023-06-13 14:34:27,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg520688a3-681f-45ad-890c-3a2d8d57de21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:34:27,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg520688a3-681f-45ad-890c-3a2d8d57de21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:34:27,241] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:34:27,241] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 14:34:27,241] [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
--------------------------------------------------------------------------------
[2023-06-13 14:34:27,243] [INFO] DFAST Taxonomy check result was written to GCA_022769885.1_ASM2276988v1_genomic.fna/tc_result.tsv
[2023-06-13 14:34:27,244] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:34:27,244] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:34:27,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg520688a3-681f-45ad-890c-3a2d8d57de21/dqc_reference/checkm_data
[2023-06-13 14:34:27,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:34:27,269] [INFO] Task started: CheckM
[2023-06-13 14:34:27,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022769885.1_ASM2276988v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022769885.1_ASM2276988v1_genomic.fna/checkm_input GCA_022769885.1_ASM2276988v1_genomic.fna/checkm_result
[2023-06-13 14:34:52,183] [INFO] Task succeeded: CheckM
[2023-06-13 14:34:52,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:34:52,204] [INFO] ===== Completeness check finished =====
[2023-06-13 14:34:52,205] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:34:52,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022769885.1_ASM2276988v1_genomic.fna/markers.fasta)
[2023-06-13 14:34:52,206] [INFO] Task started: Blastn
[2023-06-13 14:34:52,206] [INFO] Running command: blastn -query GCA_022769885.1_ASM2276988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg520688a3-681f-45ad-890c-3a2d8d57de21/dqc_reference/reference_markers_gtdb.fasta -out GCA_022769885.1_ASM2276988v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:34:52,638] [INFO] Task succeeded: Blastn
[2023-06-13 14:34:52,642] [INFO] Selected 8 target genomes.
[2023-06-13 14:34:52,643] [INFO] Target genome list was writen to GCA_022769885.1_ASM2276988v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:34:52,643] [INFO] Task started: fastANI
[2023-06-13 14:34:52,644] [INFO] Running command: fastANI --query /var/lib/cwl/stga3ec23e5-de21-4aec-8a26-525f77addb7e/GCA_022769885.1_ASM2276988v1_genomic.fna.gz --refList GCA_022769885.1_ASM2276988v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022769885.1_ASM2276988v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:34:55,166] [INFO] Task succeeded: fastANI
[2023-06-13 14:34:55,179] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:34:55,179] [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_000300255.2	s__Methanomethylophilus alvus	99.253	454	471	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	99.45	99.02	0.97	0.92	6	conclusive
GCA_002503545.1	s__Methanomethylophilus sp002503545	83.4186	289	471	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787415.1	s__Methanomethylophilus sp902787415	80.6598	163	471	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	97.47	96.90	0.79	0.76	3	-
GCA_001560915.1	s__Methanomethylophilus sp001560915	79.8314	183	471	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	96.94	96.83	0.93	0.92	3	-
GCA_902763685.1	s__Methanomethylophilus sp902763685	79.8266	175	471	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063225.1	s__Methanomethylophilus sp015063225	79.4419	157	471	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001563305.1	s__UBA71 sp001563305	78.0722	109	471	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017508065.1	s__SIG5 sp017508065	77.414	63	471	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__SIG5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:34:55,182] [INFO] GTDB search result was written to GCA_022769885.1_ASM2276988v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:34:55,183] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:34:55,195] [INFO] DFAST_QC result json was written to GCA_022769885.1_ASM2276988v1_genomic.fna/dqc_result.json
[2023-06-13 14:34:55,195] [INFO] DFAST_QC completed!
[2023-06-13 14:34:55,195] [INFO] Total running time: 0h0m44s