[2023-06-29 00:37:33,352] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:37:33,356] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:37:33,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg24703b71-b6d7-43bf-86b5-985b222ebe6d/dqc_reference
[2023-06-29 00:37:34,604] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:37:34,605] [INFO] Task started: Prodigal
[2023-06-29 00:37:34,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg96723a5f-5680-4bf3-a644-f50951aa5222/GCA_017415335.1_ASM1741533v1_genomic.fna.gz | prodigal -d GCA_017415335.1_ASM1741533v1_genomic.fna/cds.fna -a GCA_017415335.1_ASM1741533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:37:38,536] [INFO] Task succeeded: Prodigal
[2023-06-29 00:37:38,537] [INFO] Task started: HMMsearch
[2023-06-29 00:37:38,537] [INFO] Running command: hmmsearch --tblout GCA_017415335.1_ASM1741533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24703b71-b6d7-43bf-86b5-985b222ebe6d/dqc_reference/reference_markers.hmm GCA_017415335.1_ASM1741533v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:37:38,771] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:37:38,773] [INFO] Found 6/6 markers.
[2023-06-29 00:37:38,801] [INFO] Query marker FASTA was written to GCA_017415335.1_ASM1741533v1_genomic.fna/markers.fasta
[2023-06-29 00:37:38,801] [INFO] Task started: Blastn
[2023-06-29 00:37:38,801] [INFO] Running command: blastn -query GCA_017415335.1_ASM1741533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24703b71-b6d7-43bf-86b5-985b222ebe6d/dqc_reference/reference_markers.fasta -out GCA_017415335.1_ASM1741533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:37:39,435] [INFO] Task succeeded: Blastn
[2023-06-29 00:37:39,440] [INFO] Selected 17 target genomes.
[2023-06-29 00:37:39,441] [INFO] Target genome list was writen to GCA_017415335.1_ASM1741533v1_genomic.fna/target_genomes.txt
[2023-06-29 00:37:39,448] [INFO] Task started: fastANI
[2023-06-29 00:37:39,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg96723a5f-5680-4bf3-a644-f50951aa5222/GCA_017415335.1_ASM1741533v1_genomic.fna.gz --refList GCA_017415335.1_ASM1741533v1_genomic.fna/target_genomes.txt --output GCA_017415335.1_ASM1741533v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:37:50,089] [INFO] Task succeeded: fastANI
[2023-06-29 00:37:50,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24703b71-b6d7-43bf-86b5-985b222ebe6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:37:50,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24703b71-b6d7-43bf-86b5-985b222ebe6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:37:50,092] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:37:50,092] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:37:50,092] [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
--------------------------------------------------------------------------------
[2023-06-29 00:37:50,094] [INFO] DFAST Taxonomy check result was written to GCA_017415335.1_ASM1741533v1_genomic.fna/tc_result.tsv
[2023-06-29 00:37:50,096] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:37:50,096] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:37:50,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24703b71-b6d7-43bf-86b5-985b222ebe6d/dqc_reference/checkm_data
[2023-06-29 00:37:50,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:37:50,129] [INFO] Task started: CheckM
[2023-06-29 00:37:50,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017415335.1_ASM1741533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017415335.1_ASM1741533v1_genomic.fna/checkm_input GCA_017415335.1_ASM1741533v1_genomic.fna/checkm_result
[2023-06-29 00:38:09,295] [INFO] Task succeeded: CheckM
[2023-06-29 00:38:09,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:38:09,323] [INFO] ===== Completeness check finished =====
[2023-06-29 00:38:09,323] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:38:09,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017415335.1_ASM1741533v1_genomic.fna/markers.fasta)
[2023-06-29 00:38:09,324] [INFO] Task started: Blastn
[2023-06-29 00:38:09,324] [INFO] Running command: blastn -query GCA_017415335.1_ASM1741533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24703b71-b6d7-43bf-86b5-985b222ebe6d/dqc_reference/reference_markers_gtdb.fasta -out GCA_017415335.1_ASM1741533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:10,338] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:10,343] [INFO] Selected 19 target genomes.
[2023-06-29 00:38:10,343] [INFO] Target genome list was writen to GCA_017415335.1_ASM1741533v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:38:10,354] [INFO] Task started: fastANI
[2023-06-29 00:38:10,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg96723a5f-5680-4bf3-a644-f50951aa5222/GCA_017415335.1_ASM1741533v1_genomic.fna.gz --refList GCA_017415335.1_ASM1741533v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017415335.1_ASM1741533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:38:16,048] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:16,061] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:38:16,061] [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_017434845.1	s__UBA1752 sp017434845	98.2578	393	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	98.26	98.26	0.82	0.82	2	conclusive
GCA_017466805.1	s__UBA1752 sp017466805	79.741	161	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	98.43	98.43	0.89	0.89	2	-
GCA_017561145.1	s__UBA1752 sp017561145	79.4485	150	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017563195.1	s__UBA1752 sp017563195	78.8443	136	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017629895.1	s__UBA1752 sp017629895	78.813	135	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	96.45	96.45	0.78	0.78	2	-
GCA_017560145.1	s__UBA1752 sp017560145	78.7358	169	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015065165.1	s__UBA1752 sp015065165	78.4856	135	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017501055.1	s__UBA1752 sp017501055	78.2518	95	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	98.36	98.36	0.78	0.78	2	-
GCA_017630915.1	s__UBA1752 sp017630915	77.7666	104	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447445.1	s__UBA1752 sp017447445	76.6784	53	480	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1752	95.0	98.83	98.83	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-29 00:38:16,064] [INFO] GTDB search result was written to GCA_017415335.1_ASM1741533v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:38:16,065] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:38:16,068] [INFO] DFAST_QC result json was written to GCA_017415335.1_ASM1741533v1_genomic.fna/dqc_result.json
[2023-06-29 00:38:16,068] [INFO] DFAST_QC completed!
[2023-06-29 00:38:16,068] [INFO] Total running time: 0h0m43s