[2023-06-19 11:55:00,208] [INFO] DFAST_QC pipeline started.
[2023-06-19 11:55:00,213] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 11:55:00,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdba3a84-0682-4393-93e1-02808e08a689/dqc_reference
[2023-06-19 11:55:01,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 11:55:01,420] [INFO] Task started: Prodigal
[2023-06-19 11:55:01,420] [INFO] Running command: gunzip -c /var/lib/cwl/stg5245ce8e-2f8e-4800-91d9-903ac8332097/GCA_018897005.1_ASM1889700v1_genomic.fna.gz | prodigal -d GCA_018897005.1_ASM1889700v1_genomic.fna/cds.fna -a GCA_018897005.1_ASM1889700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 11:55:11,241] [INFO] Task succeeded: Prodigal
[2023-06-19 11:55:11,241] [INFO] Task started: HMMsearch
[2023-06-19 11:55:11,242] [INFO] Running command: hmmsearch --tblout GCA_018897005.1_ASM1889700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdba3a84-0682-4393-93e1-02808e08a689/dqc_reference/reference_markers.hmm GCA_018897005.1_ASM1889700v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 11:55:11,506] [INFO] Task succeeded: HMMsearch
[2023-06-19 11:55:11,508] [INFO] Found 6/6 markers.
[2023-06-19 11:55:11,542] [INFO] Query marker FASTA was written to GCA_018897005.1_ASM1889700v1_genomic.fna/markers.fasta
[2023-06-19 11:55:11,542] [INFO] Task started: Blastn
[2023-06-19 11:55:11,542] [INFO] Running command: blastn -query GCA_018897005.1_ASM1889700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdba3a84-0682-4393-93e1-02808e08a689/dqc_reference/reference_markers.fasta -out GCA_018897005.1_ASM1889700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:55:12,161] [INFO] Task succeeded: Blastn
[2023-06-19 11:55:12,166] [INFO] Selected 22 target genomes.
[2023-06-19 11:55:12,166] [INFO] Target genome list was writen to GCA_018897005.1_ASM1889700v1_genomic.fna/target_genomes.txt
[2023-06-19 11:55:12,171] [INFO] Task started: fastANI
[2023-06-19 11:55:12,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg5245ce8e-2f8e-4800-91d9-903ac8332097/GCA_018897005.1_ASM1889700v1_genomic.fna.gz --refList GCA_018897005.1_ASM1889700v1_genomic.fna/target_genomes.txt --output GCA_018897005.1_ASM1889700v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 11:55:25,952] [INFO] Task succeeded: fastANI
[2023-06-19 11:55:25,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdba3a84-0682-4393-93e1-02808e08a689/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 11:55:25,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdba3a84-0682-4393-93e1-02808e08a689/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 11:55:25,955] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 11:55:25,955] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 11:55:25,956] [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
--------------------------------------------------------------------------------
[2023-06-19 11:55:25,958] [INFO] DFAST Taxonomy check result was written to GCA_018897005.1_ASM1889700v1_genomic.fna/tc_result.tsv
[2023-06-19 11:55:25,959] [INFO] ===== Taxonomy check completed =====
[2023-06-19 11:55:25,959] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 11:55:25,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdba3a84-0682-4393-93e1-02808e08a689/dqc_reference/checkm_data
[2023-06-19 11:55:25,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 11:55:26,008] [INFO] Task started: CheckM
[2023-06-19 11:55:26,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018897005.1_ASM1889700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018897005.1_ASM1889700v1_genomic.fna/checkm_input GCA_018897005.1_ASM1889700v1_genomic.fna/checkm_result
[2023-06-19 11:55:59,430] [INFO] Task succeeded: CheckM
[2023-06-19 11:55:59,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 11:55:59,456] [INFO] ===== Completeness check finished =====
[2023-06-19 11:55:59,457] [INFO] ===== Start GTDB Search =====
[2023-06-19 11:55:59,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018897005.1_ASM1889700v1_genomic.fna/markers.fasta)
[2023-06-19 11:55:59,458] [INFO] Task started: Blastn
[2023-06-19 11:55:59,458] [INFO] Running command: blastn -query GCA_018897005.1_ASM1889700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdba3a84-0682-4393-93e1-02808e08a689/dqc_reference/reference_markers_gtdb.fasta -out GCA_018897005.1_ASM1889700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:56:00,303] [INFO] Task succeeded: Blastn
[2023-06-19 11:56:00,307] [INFO] Selected 17 target genomes.
[2023-06-19 11:56:00,308] [INFO] Target genome list was writen to GCA_018897005.1_ASM1889700v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 11:56:00,341] [INFO] Task started: fastANI
[2023-06-19 11:56:00,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg5245ce8e-2f8e-4800-91d9-903ac8332097/GCA_018897005.1_ASM1889700v1_genomic.fna.gz --refList GCA_018897005.1_ASM1889700v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018897005.1_ASM1889700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 11:56:12,215] [INFO] Task succeeded: fastANI
[2023-06-19 11:56:12,224] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 11:56:12,225] [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_018898455.1	s__JAHIJO01 sp018898455	99.9712	1049	1116	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__JAAZAB01;f__VSJD01;g__JAHIJO01	95.0	99.93	99.88	0.95	0.94	4	conclusive
GCA_008636095.1	s__VSJD01 sp008636095	78.4066	199	1116	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__JAAZAB01;f__VSJD01;g__VSJD01	95.0	99.74	99.73	0.88	0.86	5	-
GCA_018896395.1	s__VSJD01 sp018896395	78.0223	94	1116	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__JAAZAB01;f__VSJD01;g__VSJD01	95.0	98.50	98.47	0.77	0.75	3	-
GCA_016188985.1	s__VSJD01 sp016188985	76.1025	97	1116	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__JAAZAB01;f__VSJD01;g__VSJD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 11:56:12,227] [INFO] GTDB search result was written to GCA_018897005.1_ASM1889700v1_genomic.fna/result_gtdb.tsv
[2023-06-19 11:56:12,227] [INFO] ===== GTDB Search completed =====
[2023-06-19 11:56:12,230] [INFO] DFAST_QC result json was written to GCA_018897005.1_ASM1889700v1_genomic.fna/dqc_result.json
[2023-06-19 11:56:12,230] [INFO] DFAST_QC completed!
[2023-06-19 11:56:12,231] [INFO] Total running time: 0h1m12s