[2023-06-05 07:15:51,265] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:15:51,280] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:15:51,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a996a84-82d6-4e86-897f-cc176dc16d29/dqc_reference
[2023-06-05 07:15:52,928] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:15:52,929] [INFO] Task started: Prodigal
[2023-06-05 07:15:52,929] [INFO] Running command: gunzip -c /var/lib/cwl/stg57e94a37-413b-413d-be31-60743c6dcb25/GCA_001798005.1_ASM179800v1_genomic.fna.gz | prodigal -d GCA_001798005.1_ASM179800v1_genomic.fna/cds.fna -a GCA_001798005.1_ASM179800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:15:57,794] [INFO] Task succeeded: Prodigal
[2023-06-05 07:15:57,795] [INFO] Task started: HMMsearch
[2023-06-05 07:15:57,795] [INFO] Running command: hmmsearch --tblout GCA_001798005.1_ASM179800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a996a84-82d6-4e86-897f-cc176dc16d29/dqc_reference/reference_markers.hmm GCA_001798005.1_ASM179800v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:15:58,051] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:15:58,053] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg57e94a37-413b-413d-be31-60743c6dcb25/GCA_001798005.1_ASM179800v1_genomic.fna.gz]
[2023-06-05 07:15:58,079] [INFO] Query marker FASTA was written to GCA_001798005.1_ASM179800v1_genomic.fna/markers.fasta
[2023-06-05 07:15:58,080] [INFO] Task started: Blastn
[2023-06-05 07:15:58,080] [INFO] Running command: blastn -query GCA_001798005.1_ASM179800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a996a84-82d6-4e86-897f-cc176dc16d29/dqc_reference/reference_markers.fasta -out GCA_001798005.1_ASM179800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:15:58,737] [INFO] Task succeeded: Blastn
[2023-06-05 07:15:58,756] [INFO] Selected 19 target genomes.
[2023-06-05 07:15:58,757] [INFO] Target genome list was writen to GCA_001798005.1_ASM179800v1_genomic.fna/target_genomes.txt
[2023-06-05 07:15:58,762] [INFO] Task started: fastANI
[2023-06-05 07:15:58,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e94a37-413b-413d-be31-60743c6dcb25/GCA_001798005.1_ASM179800v1_genomic.fna.gz --refList GCA_001798005.1_ASM179800v1_genomic.fna/target_genomes.txt --output GCA_001798005.1_ASM179800v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:16:12,912] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:12,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a996a84-82d6-4e86-897f-cc176dc16d29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:16:12,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a996a84-82d6-4e86-897f-cc176dc16d29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:16:12,915] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:16:12,915] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 07:16:12,915] [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 07:16:12,918] [INFO] DFAST Taxonomy check result was written to GCA_001798005.1_ASM179800v1_genomic.fna/tc_result.tsv
[2023-06-05 07:16:12,919] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:16:12,919] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:16:12,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a996a84-82d6-4e86-897f-cc176dc16d29/dqc_reference/checkm_data
[2023-06-05 07:16:12,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:16:12,956] [INFO] Task started: CheckM
[2023-06-05 07:16:12,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001798005.1_ASM179800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001798005.1_ASM179800v1_genomic.fna/checkm_input GCA_001798005.1_ASM179800v1_genomic.fna/checkm_result
[2023-06-05 07:16:32,250] [INFO] Task succeeded: CheckM
[2023-06-05 07:16:32,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:16:32,274] [INFO] ===== Completeness check finished =====
[2023-06-05 07:16:32,274] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:16:32,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001798005.1_ASM179800v1_genomic.fna/markers.fasta)
[2023-06-05 07:16:32,275] [INFO] Task started: Blastn
[2023-06-05 07:16:32,275] [INFO] Running command: blastn -query GCA_001798005.1_ASM179800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a996a84-82d6-4e86-897f-cc176dc16d29/dqc_reference/reference_markers_gtdb.fasta -out GCA_001798005.1_ASM179800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:33,025] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:33,031] [INFO] Selected 24 target genomes.
[2023-06-05 07:16:33,031] [INFO] Target genome list was writen to GCA_001798005.1_ASM179800v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:16:33,294] [INFO] Task started: fastANI
[2023-06-05 07:16:33,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e94a37-413b-413d-be31-60743c6dcb25/GCA_001798005.1_ASM179800v1_genomic.fna.gz --refList GCA_001798005.1_ASM179800v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001798005.1_ASM179800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:16:47,389] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:47,395] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 07:16:47,396] [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_016875165.1	s__JAHJQK01 sp016875165	78.4111	224	613	d__Bacteria;p__Desulfobacterota;c__SM23-61;o__SM23-61;f__SM23-61;g__JAHJQK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819135.1	s__JAHJQK01 sp018819135	78.3401	190	613	d__Bacteria;p__Desulfobacterota;c__SM23-61;o__SM23-61;f__SM23-61;g__JAHJQK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234425.1	s__JACRCA01 sp016234425	76.8701	117	613	d__Bacteria;p__Desulfobacterota;c__SM23-61;o__SM23-61;f__SM23-61;g__JACRCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001304105.1	s__SM23-61 sp001304105	76.8023	102	613	d__Bacteria;p__Desulfobacterota;c__SM23-61;o__SM23-61;f__SM23-61;g__SM23-61	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388675.1	s__SM23-61 sp013388675	76.3825	106	613	d__Bacteria;p__Desulfobacterota;c__SM23-61;o__SM23-61;f__SM23-61;g__SM23-61	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:16:47,398] [INFO] GTDB search result was written to GCA_001798005.1_ASM179800v1_genomic.fna/result_gtdb.tsv
[2023-06-05 07:16:47,399] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:16:47,402] [INFO] DFAST_QC result json was written to GCA_001798005.1_ASM179800v1_genomic.fna/dqc_result.json
[2023-06-05 07:16:47,402] [INFO] DFAST_QC completed!
[2023-06-05 07:16:47,402] [INFO] Total running time: 0h0m56s