[2023-06-18 20:10:45,060] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:10:45,069] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:10:45,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b032b14-50d0-4fac-bd87-523b7316fbbb/dqc_reference
[2023-06-18 20:10:46,953] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:10:46,955] [INFO] Task started: Prodigal
[2023-06-18 20:10:46,956] [INFO] Running command: gunzip -c /var/lib/cwl/stgef5ac74b-2c62-456b-9747-582c790116cc/GCA_014874265.1_ASM1487426v1_genomic.fna.gz | prodigal -d GCA_014874265.1_ASM1487426v1_genomic.fna/cds.fna -a GCA_014874265.1_ASM1487426v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:10:51,807] [INFO] Task succeeded: Prodigal
[2023-06-18 20:10:51,808] [INFO] Task started: HMMsearch
[2023-06-18 20:10:51,808] [INFO] Running command: hmmsearch --tblout GCA_014874265.1_ASM1487426v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b032b14-50d0-4fac-bd87-523b7316fbbb/dqc_reference/reference_markers.hmm GCA_014874265.1_ASM1487426v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:10:52,057] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:10:52,058] [INFO] Found 6/6 markers.
[2023-06-18 20:10:52,078] [INFO] Query marker FASTA was written to GCA_014874265.1_ASM1487426v1_genomic.fna/markers.fasta
[2023-06-18 20:10:52,079] [INFO] Task started: Blastn
[2023-06-18 20:10:52,079] [INFO] Running command: blastn -query GCA_014874265.1_ASM1487426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b032b14-50d0-4fac-bd87-523b7316fbbb/dqc_reference/reference_markers.fasta -out GCA_014874265.1_ASM1487426v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:10:52,686] [INFO] Task succeeded: Blastn
[2023-06-18 20:10:52,693] [INFO] Selected 23 target genomes.
[2023-06-18 20:10:52,694] [INFO] Target genome list was writen to GCA_014874265.1_ASM1487426v1_genomic.fna/target_genomes.txt
[2023-06-18 20:10:52,699] [INFO] Task started: fastANI
[2023-06-18 20:10:52,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgef5ac74b-2c62-456b-9747-582c790116cc/GCA_014874265.1_ASM1487426v1_genomic.fna.gz --refList GCA_014874265.1_ASM1487426v1_genomic.fna/target_genomes.txt --output GCA_014874265.1_ASM1487426v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:11:07,663] [INFO] Task succeeded: fastANI
[2023-06-18 20:11:07,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b032b14-50d0-4fac-bd87-523b7316fbbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:11:07,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b032b14-50d0-4fac-bd87-523b7316fbbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:11:07,666] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:11:07,666] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:11:07,667] [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
--------------------------------------------------------------------------------
[2023-06-18 20:11:07,669] [INFO] DFAST Taxonomy check result was written to GCA_014874265.1_ASM1487426v1_genomic.fna/tc_result.tsv
[2023-06-18 20:11:07,670] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:11:07,670] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:11:07,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b032b14-50d0-4fac-bd87-523b7316fbbb/dqc_reference/checkm_data
[2023-06-18 20:11:07,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:11:07,701] [INFO] Task started: CheckM
[2023-06-18 20:11:07,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014874265.1_ASM1487426v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014874265.1_ASM1487426v1_genomic.fna/checkm_input GCA_014874265.1_ASM1487426v1_genomic.fna/checkm_result
[2023-06-18 20:11:29,053] [INFO] Task succeeded: CheckM
[2023-06-18 20:11:29,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:11:29,078] [INFO] ===== Completeness check finished =====
[2023-06-18 20:11:29,078] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:11:29,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014874265.1_ASM1487426v1_genomic.fna/markers.fasta)
[2023-06-18 20:11:29,079] [INFO] Task started: Blastn
[2023-06-18 20:11:29,079] [INFO] Running command: blastn -query GCA_014874265.1_ASM1487426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b032b14-50d0-4fac-bd87-523b7316fbbb/dqc_reference/reference_markers_gtdb.fasta -out GCA_014874265.1_ASM1487426v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:11:29,975] [INFO] Task succeeded: Blastn
[2023-06-18 20:11:29,980] [INFO] Selected 17 target genomes.
[2023-06-18 20:11:29,980] [INFO] Target genome list was writen to GCA_014874265.1_ASM1487426v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:11:29,991] [INFO] Task started: fastANI
[2023-06-18 20:11:29,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgef5ac74b-2c62-456b-9747-582c790116cc/GCA_014874265.1_ASM1487426v1_genomic.fna.gz --refList GCA_014874265.1_ASM1487426v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014874265.1_ASM1487426v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:11:37,742] [INFO] Task succeeded: fastANI
[2023-06-18 20:11:37,754] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:11:37,754] [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_014874265.1	s__JACWAD01 sp014874265	100.0	603	610	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__JACWAD01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014874175.1	s__JACWAD01 sp014874175	77.9018	149	610	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__JACWAD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599855.1	s__SURF-19 sp003599855	77.215	103	610	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__SURF-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859345.1	s__Kmv30 sp014859345	76.9484	74	610	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__Kmv30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235065.1	s__JACRMB01 sp016235065	76.6033	102	610	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__JACRMB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002897715.1	s__BMS3ABIN01 sp002897715	76.591	60	610	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__BMS3ABIN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650015.1	s__JACRMB01 sp016650015	76.5459	69	610	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__BMS3ABIN01;f__BMS3ABIN01;g__JACRMB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:11:37,757] [INFO] GTDB search result was written to GCA_014874265.1_ASM1487426v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:11:37,758] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:11:37,760] [INFO] DFAST_QC result json was written to GCA_014874265.1_ASM1487426v1_genomic.fna/dqc_result.json
[2023-06-18 20:11:37,761] [INFO] DFAST_QC completed!
[2023-06-18 20:11:37,761] [INFO] Total running time: 0h0m53s