[2023-06-05 18:44:28,529] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:44:28,531] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:44:28,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg586a339c-1c2e-4e3c-8494-e18f007ba415/dqc_reference
[2023-06-05 18:44:29,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:44:29,647] [INFO] Task started: Prodigal
[2023-06-05 18:44:29,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg26c112f6-e22e-420e-88e2-6af3e0345414/GCA_004321925.1_ASM432192v1_genomic.fna.gz | prodigal -d GCA_004321925.1_ASM432192v1_genomic.fna/cds.fna -a GCA_004321925.1_ASM432192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:44:36,531] [INFO] Task succeeded: Prodigal
[2023-06-05 18:44:36,532] [INFO] Task started: HMMsearch
[2023-06-05 18:44:36,532] [INFO] Running command: hmmsearch --tblout GCA_004321925.1_ASM432192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg586a339c-1c2e-4e3c-8494-e18f007ba415/dqc_reference/reference_markers.hmm GCA_004321925.1_ASM432192v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:44:36,759] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:44:36,760] [INFO] Found 6/6 markers.
[2023-06-05 18:44:36,788] [INFO] Query marker FASTA was written to GCA_004321925.1_ASM432192v1_genomic.fna/markers.fasta
[2023-06-05 18:44:36,788] [INFO] Task started: Blastn
[2023-06-05 18:44:36,788] [INFO] Running command: blastn -query GCA_004321925.1_ASM432192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg586a339c-1c2e-4e3c-8494-e18f007ba415/dqc_reference/reference_markers.fasta -out GCA_004321925.1_ASM432192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:44:37,388] [INFO] Task succeeded: Blastn
[2023-06-05 18:44:37,392] [INFO] Selected 26 target genomes.
[2023-06-05 18:44:37,392] [INFO] Target genome list was writen to GCA_004321925.1_ASM432192v1_genomic.fna/target_genomes.txt
[2023-06-05 18:44:37,400] [INFO] Task started: fastANI
[2023-06-05 18:44:37,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c112f6-e22e-420e-88e2-6af3e0345414/GCA_004321925.1_ASM432192v1_genomic.fna.gz --refList GCA_004321925.1_ASM432192v1_genomic.fna/target_genomes.txt --output GCA_004321925.1_ASM432192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:44:53,375] [INFO] Task succeeded: fastANI
[2023-06-05 18:44:53,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg586a339c-1c2e-4e3c-8494-e18f007ba415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:44:53,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg586a339c-1c2e-4e3c-8494-e18f007ba415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:44:53,377] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:44:53,377] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:44:53,377] [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
--------------------------------------------------------------------------------
[2023-06-05 18:44:53,379] [INFO] DFAST Taxonomy check result was written to GCA_004321925.1_ASM432192v1_genomic.fna/tc_result.tsv
[2023-06-05 18:44:53,379] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:44:53,379] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:44:53,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg586a339c-1c2e-4e3c-8494-e18f007ba415/dqc_reference/checkm_data
[2023-06-05 18:44:53,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:44:53,417] [INFO] Task started: CheckM
[2023-06-05 18:44:53,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004321925.1_ASM432192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004321925.1_ASM432192v1_genomic.fna/checkm_input GCA_004321925.1_ASM432192v1_genomic.fna/checkm_result
[2023-06-05 18:45:20,021] [INFO] Task succeeded: CheckM
[2023-06-05 18:45:20,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:45:20,050] [INFO] ===== Completeness check finished =====
[2023-06-05 18:45:20,050] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:45:20,051] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004321925.1_ASM432192v1_genomic.fna/markers.fasta)
[2023-06-05 18:45:20,051] [INFO] Task started: Blastn
[2023-06-05 18:45:20,051] [INFO] Running command: blastn -query GCA_004321925.1_ASM432192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg586a339c-1c2e-4e3c-8494-e18f007ba415/dqc_reference/reference_markers_gtdb.fasta -out GCA_004321925.1_ASM432192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:45:21,087] [INFO] Task succeeded: Blastn
[2023-06-05 18:45:21,090] [INFO] Selected 23 target genomes.
[2023-06-05 18:45:21,090] [INFO] Target genome list was writen to GCA_004321925.1_ASM432192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:45:21,249] [INFO] Task started: fastANI
[2023-06-05 18:45:21,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c112f6-e22e-420e-88e2-6af3e0345414/GCA_004321925.1_ASM432192v1_genomic.fna.gz --refList GCA_004321925.1_ASM432192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004321925.1_ASM432192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:45:37,469] [INFO] Task succeeded: fastANI
[2023-06-05 18:45:37,477] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:45:37,477] [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_004321925.1	s__PALSA-1316 sp004321925	99.9999	1006	1015	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA6898;g__PALSA-1316	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016215155.1	s__PALSA-1316 sp016215155	78.0711	225	1015	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA6898;g__PALSA-1316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824615.1	s__PALSA-1316 sp013824615	77.5868	218	1015	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA6898;g__PALSA-1316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214855.1	s__UBA6898 sp016214855	77.0672	131	1015	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA6898;g__UBA6898	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016217675.1	s__UBA6898 sp016217675	76.9761	122	1015	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA6898;g__UBA6898	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252075.1	s__UBA6898 sp003252075	76.8303	74	1015	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA6898;g__UBA6898	95.0	99.66	99.66	0.91	0.91	2	-
GCA_003153275.1	s__PALSA-1316 sp003153275	76.6851	119	1015	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA6898;g__PALSA-1316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026685.1	s__UBA6898 sp012026685	76.5831	93	1015	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA6898;g__UBA6898	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:45:37,481] [INFO] GTDB search result was written to GCA_004321925.1_ASM432192v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:45:37,482] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:45:37,484] [INFO] DFAST_QC result json was written to GCA_004321925.1_ASM432192v1_genomic.fna/dqc_result.json
[2023-06-05 18:45:37,484] [INFO] DFAST_QC completed!
[2023-06-05 18:45:37,484] [INFO] Total running time: 0h1m9s