[2023-06-26 20:47:38,586] [INFO] DFAST_QC pipeline started.
[2023-06-26 20:47:38,588] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 20:47:38,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg0337344c-3368-4d6b-bc93-03b3572036ff/dqc_reference
[2023-06-26 20:47:40,255] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 20:47:40,256] [INFO] Task started: Prodigal
[2023-06-26 20:47:40,256] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc6acba3-07c3-4afa-8644-ece3c53dd9ea/GCA_002472355.1_ASM247235v1_genomic.fna.gz | prodigal -d GCA_002472355.1_ASM247235v1_genomic.fna/cds.fna -a GCA_002472355.1_ASM247235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 20:47:43,636] [INFO] Task succeeded: Prodigal
[2023-06-26 20:47:43,637] [INFO] Task started: HMMsearch
[2023-06-26 20:47:43,637] [INFO] Running command: hmmsearch --tblout GCA_002472355.1_ASM247235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0337344c-3368-4d6b-bc93-03b3572036ff/dqc_reference/reference_markers.hmm GCA_002472355.1_ASM247235v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 20:47:43,850] [INFO] Task succeeded: HMMsearch
[2023-06-26 20:47:43,851] [INFO] Found 6/6 markers.
[2023-06-26 20:47:44,007] [INFO] Query marker FASTA was written to GCA_002472355.1_ASM247235v1_genomic.fna/markers.fasta
[2023-06-26 20:47:44,007] [INFO] Task started: Blastn
[2023-06-26 20:47:44,007] [INFO] Running command: blastn -query GCA_002472355.1_ASM247235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0337344c-3368-4d6b-bc93-03b3572036ff/dqc_reference/reference_markers.fasta -out GCA_002472355.1_ASM247235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 20:47:44,572] [INFO] Task succeeded: Blastn
[2023-06-26 20:47:44,575] [INFO] Selected 20 target genomes.
[2023-06-26 20:47:44,576] [INFO] Target genome list was writen to GCA_002472355.1_ASM247235v1_genomic.fna/target_genomes.txt
[2023-06-26 20:47:44,583] [INFO] Task started: fastANI
[2023-06-26 20:47:44,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc6acba3-07c3-4afa-8644-ece3c53dd9ea/GCA_002472355.1_ASM247235v1_genomic.fna.gz --refList GCA_002472355.1_ASM247235v1_genomic.fna/target_genomes.txt --output GCA_002472355.1_ASM247235v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 20:47:54,575] [INFO] Task succeeded: fastANI
[2023-06-26 20:47:54,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0337344c-3368-4d6b-bc93-03b3572036ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 20:47:54,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0337344c-3368-4d6b-bc93-03b3572036ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 20:47:54,577] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 20:47:54,577] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-26 20:47:54,577] [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
--------------------------------------------------------------------------------
[2023-06-26 20:47:54,579] [INFO] DFAST Taxonomy check result was written to GCA_002472355.1_ASM247235v1_genomic.fna/tc_result.tsv
[2023-06-26 20:47:54,579] [INFO] ===== Taxonomy check completed =====
[2023-06-26 20:47:54,579] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 20:47:54,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0337344c-3368-4d6b-bc93-03b3572036ff/dqc_reference/checkm_data
[2023-06-26 20:47:54,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 20:47:54,624] [INFO] Task started: CheckM
[2023-06-26 20:47:54,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002472355.1_ASM247235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002472355.1_ASM247235v1_genomic.fna/checkm_input GCA_002472355.1_ASM247235v1_genomic.fna/checkm_result
[2023-06-26 20:48:10,902] [INFO] Task succeeded: CheckM
[2023-06-26 20:48:10,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 20:48:10,922] [INFO] ===== Completeness check finished =====
[2023-06-26 20:48:10,923] [INFO] ===== Start GTDB Search =====
[2023-06-26 20:48:10,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002472355.1_ASM247235v1_genomic.fna/markers.fasta)
[2023-06-26 20:48:10,924] [INFO] Task started: Blastn
[2023-06-26 20:48:10,924] [INFO] Running command: blastn -query GCA_002472355.1_ASM247235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0337344c-3368-4d6b-bc93-03b3572036ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_002472355.1_ASM247235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 20:48:11,674] [INFO] Task succeeded: Blastn
[2023-06-26 20:48:11,677] [INFO] Selected 17 target genomes.
[2023-06-26 20:48:11,677] [INFO] Target genome list was writen to GCA_002472355.1_ASM247235v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 20:48:11,682] [INFO] Task started: fastANI
[2023-06-26 20:48:11,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc6acba3-07c3-4afa-8644-ece3c53dd9ea/GCA_002472355.1_ASM247235v1_genomic.fna.gz --refList GCA_002472355.1_ASM247235v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002472355.1_ASM247235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 20:48:17,665] [INFO] Task succeeded: fastANI
[2023-06-26 20:48:17,675] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 20:48:17,676] [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_900319365.1	s__UBA2813 sp900319365	99.5086	534	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	99.78	99.51	0.97	0.93	7	conclusive
GCA_902794035.1	s__UBA2813 sp902794035	78.3856	196	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774905.1	s__UBA2813 sp902774905	78.2444	237	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	97.89	97.89	0.91	0.91	2	-
GCA_902792085.1	s__UBA2813 sp902792085	78.2066	231	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470815.1	s__UBA2813 sp017470815	78.108	225	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777855.1	s__UBA2813 sp902777855	77.9377	214	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361485.1	s__UBA2813 sp002361485	77.8954	191	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	97.91	97.91	0.90	0.90	2	-
GCA_902802825.1	s__UBA2813 sp902802825	77.8707	181	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788345.1	s__UBA2813 sp902788345	77.8316	191	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791985.1	s__UBA2813 sp902791985	77.6144	197	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558955.1	s__Zag111 sp004558955	77.4975	111	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	98.49	98.49	0.77	0.77	2	-
GCA_902766975.1	s__UBA2813 sp902766975	77.3652	170	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	98.60	98.29	0.95	0.95	3	-
GCA_002102825.1	s__Zag111 sp002102825	77.2553	135	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.43	98.83	0.94	0.90	9	-
GCA_902766105.1	s__Zag111 sp902766105	76.9563	130	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766395.1	s__UBA2813 sp902766395	76.7996	132	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437435.1	s__Stercorousia sp000437435	76.6957	89	569	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	97.52	97.52	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-26 20:48:17,677] [INFO] GTDB search result was written to GCA_002472355.1_ASM247235v1_genomic.fna/result_gtdb.tsv
[2023-06-26 20:48:17,678] [INFO] ===== GTDB Search completed =====
[2023-06-26 20:48:17,680] [INFO] DFAST_QC result json was written to GCA_002472355.1_ASM247235v1_genomic.fna/dqc_result.json
[2023-06-26 20:48:17,680] [INFO] DFAST_QC completed!
[2023-06-26 20:48:17,680] [INFO] Total running time: 0h0m39s