[2023-06-28 22:57:15,676] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:57:15,678] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:57:15,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg726d960c-a13e-46f2-9b8e-3f9599b95c71/dqc_reference
[2023-06-28 22:57:16,892] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:57:16,893] [INFO] Task started: Prodigal
[2023-06-28 22:57:16,893] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2e912b8-43f0-48d9-bc07-e7626d4af4ec/GCA_012517865.1_ASM1251786v1_genomic.fna.gz | prodigal -d GCA_012517865.1_ASM1251786v1_genomic.fna/cds.fna -a GCA_012517865.1_ASM1251786v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:57:22,018] [INFO] Task succeeded: Prodigal
[2023-06-28 22:57:22,019] [INFO] Task started: HMMsearch
[2023-06-28 22:57:22,019] [INFO] Running command: hmmsearch --tblout GCA_012517865.1_ASM1251786v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg726d960c-a13e-46f2-9b8e-3f9599b95c71/dqc_reference/reference_markers.hmm GCA_012517865.1_ASM1251786v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:57:22,262] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:57:22,264] [INFO] Found 6/6 markers.
[2023-06-28 22:57:22,286] [INFO] Query marker FASTA was written to GCA_012517865.1_ASM1251786v1_genomic.fna/markers.fasta
[2023-06-28 22:57:22,287] [INFO] Task started: Blastn
[2023-06-28 22:57:22,287] [INFO] Running command: blastn -query GCA_012517865.1_ASM1251786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg726d960c-a13e-46f2-9b8e-3f9599b95c71/dqc_reference/reference_markers.fasta -out GCA_012517865.1_ASM1251786v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:57:22,854] [INFO] Task succeeded: Blastn
[2023-06-28 22:57:22,858] [INFO] Selected 20 target genomes.
[2023-06-28 22:57:22,858] [INFO] Target genome list was writen to GCA_012517865.1_ASM1251786v1_genomic.fna/target_genomes.txt
[2023-06-28 22:57:22,861] [INFO] Task started: fastANI
[2023-06-28 22:57:22,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e912b8-43f0-48d9-bc07-e7626d4af4ec/GCA_012517865.1_ASM1251786v1_genomic.fna.gz --refList GCA_012517865.1_ASM1251786v1_genomic.fna/target_genomes.txt --output GCA_012517865.1_ASM1251786v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:57:36,088] [INFO] Task succeeded: fastANI
[2023-06-28 22:57:36,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg726d960c-a13e-46f2-9b8e-3f9599b95c71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:57:36,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg726d960c-a13e-46f2-9b8e-3f9599b95c71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:57:36,091] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:57:36,091] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 22:57:36,092] [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
--------------------------------------------------------------------------------
[2023-06-28 22:57:36,094] [INFO] DFAST Taxonomy check result was written to GCA_012517865.1_ASM1251786v1_genomic.fna/tc_result.tsv
[2023-06-28 22:57:36,095] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:57:36,096] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:57:36,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg726d960c-a13e-46f2-9b8e-3f9599b95c71/dqc_reference/checkm_data
[2023-06-28 22:57:36,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:57:36,123] [INFO] Task started: CheckM
[2023-06-28 22:57:36,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012517865.1_ASM1251786v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012517865.1_ASM1251786v1_genomic.fna/checkm_input GCA_012517865.1_ASM1251786v1_genomic.fna/checkm_result
[2023-06-28 22:57:57,694] [INFO] Task succeeded: CheckM
[2023-06-28 22:57:57,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:57:57,717] [INFO] ===== Completeness check finished =====
[2023-06-28 22:57:57,718] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:57:57,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012517865.1_ASM1251786v1_genomic.fna/markers.fasta)
[2023-06-28 22:57:57,718] [INFO] Task started: Blastn
[2023-06-28 22:57:57,719] [INFO] Running command: blastn -query GCA_012517865.1_ASM1251786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg726d960c-a13e-46f2-9b8e-3f9599b95c71/dqc_reference/reference_markers_gtdb.fasta -out GCA_012517865.1_ASM1251786v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:57:58,507] [INFO] Task succeeded: Blastn
[2023-06-28 22:57:58,513] [INFO] Selected 19 target genomes.
[2023-06-28 22:57:58,513] [INFO] Target genome list was writen to GCA_012517865.1_ASM1251786v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:57:58,525] [INFO] Task started: fastANI
[2023-06-28 22:57:58,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e912b8-43f0-48d9-bc07-e7626d4af4ec/GCA_012517865.1_ASM1251786v1_genomic.fna.gz --refList GCA_012517865.1_ASM1251786v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012517865.1_ASM1251786v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:58:08,624] [INFO] Task succeeded: fastANI
[2023-06-28 22:58:08,635] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:58:08,636] [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_012517865.1	s__49-20 sp012517865	100.0	609	611	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__49-20	95.0	99.82	99.82	0.88	0.88	2	conclusive
GCA_012797215.1	s__49-20 sp012797215	81.0103	294	611	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__49-20	95.0	99.20	99.20	0.92	0.92	2	-
GCA_002436085.1	s__49-20 sp002436085	80.0157	384	611	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__49-20	95.0	96.28	96.28	0.91	0.91	2	-
GCA_003445715.1	s__49-20 sp003445715	76.2833	67	611	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__49-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002306055.1	s__T78 sp002306055	76.1898	53	611	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__T78	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:58:08,638] [INFO] GTDB search result was written to GCA_012517865.1_ASM1251786v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:58:08,639] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:58:08,642] [INFO] DFAST_QC result json was written to GCA_012517865.1_ASM1251786v1_genomic.fna/dqc_result.json
[2023-06-28 22:58:08,642] [INFO] DFAST_QC completed!
[2023-06-28 22:58:08,642] [INFO] Total running time: 0h0m53s