[2023-06-27 15:01:16,121] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:01:16,126] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:01:16,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dc15252-3a54-40ed-b795-fe271df50f55/dqc_reference
[2023-06-27 15:01:17,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:01:17,370] [INFO] Task started: Prodigal
[2023-06-27 15:01:17,370] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3dcbe76-6484-47e8-8b1f-b50b92b95685/GCA_026708765.1_ASM2670876v1_genomic.fna.gz | prodigal -d GCA_026708765.1_ASM2670876v1_genomic.fna/cds.fna -a GCA_026708765.1_ASM2670876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:01:20,167] [INFO] Task succeeded: Prodigal
[2023-06-27 15:01:20,167] [INFO] Task started: HMMsearch
[2023-06-27 15:01:20,168] [INFO] Running command: hmmsearch --tblout GCA_026708765.1_ASM2670876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dc15252-3a54-40ed-b795-fe271df50f55/dqc_reference/reference_markers.hmm GCA_026708765.1_ASM2670876v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:01:20,313] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:01:20,315] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc3dcbe76-6484-47e8-8b1f-b50b92b95685/GCA_026708765.1_ASM2670876v1_genomic.fna.gz]
[2023-06-27 15:01:20,333] [INFO] Query marker FASTA was written to GCA_026708765.1_ASM2670876v1_genomic.fna/markers.fasta
[2023-06-27 15:01:20,334] [INFO] Task started: Blastn
[2023-06-27 15:01:20,334] [INFO] Running command: blastn -query GCA_026708765.1_ASM2670876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc15252-3a54-40ed-b795-fe271df50f55/dqc_reference/reference_markers.fasta -out GCA_026708765.1_ASM2670876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:01:21,213] [INFO] Task succeeded: Blastn
[2023-06-27 15:01:21,217] [INFO] Selected 7 target genomes.
[2023-06-27 15:01:21,217] [INFO] Target genome list was writen to GCA_026708765.1_ASM2670876v1_genomic.fna/target_genomes.txt
[2023-06-27 15:01:21,219] [INFO] Task started: fastANI
[2023-06-27 15:01:21,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3dcbe76-6484-47e8-8b1f-b50b92b95685/GCA_026708765.1_ASM2670876v1_genomic.fna.gz --refList GCA_026708765.1_ASM2670876v1_genomic.fna/target_genomes.txt --output GCA_026708765.1_ASM2670876v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:01:26,047] [INFO] Task succeeded: fastANI
[2023-06-27 15:01:26,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dc15252-3a54-40ed-b795-fe271df50f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:01:26,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dc15252-3a54-40ed-b795-fe271df50f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:01:26,050] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:01:26,050] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 15:01:26,050] [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
--------------------------------------------------------------------------------
[2023-06-27 15:01:26,053] [INFO] DFAST Taxonomy check result was written to GCA_026708765.1_ASM2670876v1_genomic.fna/tc_result.tsv
[2023-06-27 15:01:26,054] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:01:26,054] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:01:26,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dc15252-3a54-40ed-b795-fe271df50f55/dqc_reference/checkm_data
[2023-06-27 15:01:26,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:01:26,076] [INFO] Task started: CheckM
[2023-06-27 15:01:26,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708765.1_ASM2670876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708765.1_ASM2670876v1_genomic.fna/checkm_input GCA_026708765.1_ASM2670876v1_genomic.fna/checkm_result
[2023-06-27 15:01:41,514] [INFO] Task succeeded: CheckM
[2023-06-27 15:01:41,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.27%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-27 15:01:41,541] [INFO] ===== Completeness check finished =====
[2023-06-27 15:01:41,542] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:01:41,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708765.1_ASM2670876v1_genomic.fna/markers.fasta)
[2023-06-27 15:01:41,542] [INFO] Task started: Blastn
[2023-06-27 15:01:41,543] [INFO] Running command: blastn -query GCA_026708765.1_ASM2670876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc15252-3a54-40ed-b795-fe271df50f55/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708765.1_ASM2670876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:01:41,968] [INFO] Task succeeded: Blastn
[2023-06-27 15:01:41,972] [INFO] Selected 10 target genomes.
[2023-06-27 15:01:41,972] [INFO] Target genome list was writen to GCA_026708765.1_ASM2670876v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:01:41,975] [INFO] Task started: fastANI
[2023-06-27 15:01:41,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3dcbe76-6484-47e8-8b1f-b50b92b95685/GCA_026708765.1_ASM2670876v1_genomic.fna.gz --refList GCA_026708765.1_ASM2670876v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708765.1_ASM2670876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:01:46,225] [INFO] Task succeeded: fastANI
[2023-06-27 15:01:46,229] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 15:01:46,230] [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_009837205.1	s__RKRQ01 sp009837205	80.497	232	330	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__RKRQ01;f__RKRQ01;g__RKRQ01	95.0	98.20	97.22	0.91	0.89	4	-
GCA_009840385.1	s__RKRQ01 sp009840385	79.8347	203	330	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__RKRQ01;f__RKRQ01;g__RKRQ01	95.0	96.93	96.24	0.92	0.88	7	-
GCA_007571325.1	s__RKRQ01 sp007571325	78.2605	113	330	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__RKRQ01;f__RKRQ01;g__RKRQ01	95.0	98.96	98.96	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-27 15:01:46,232] [INFO] GTDB search result was written to GCA_026708765.1_ASM2670876v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:01:46,232] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:01:46,235] [INFO] DFAST_QC result json was written to GCA_026708765.1_ASM2670876v1_genomic.fna/dqc_result.json
[2023-06-27 15:01:46,235] [INFO] DFAST_QC completed!
[2023-06-27 15:01:46,235] [INFO] Total running time: 0h0m30s