[2023-07-01 00:24:00,966] [INFO] DFAST_QC pipeline started.
[2023-07-01 00:24:00,969] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 00:24:00,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg683f455f-c027-4441-9d1b-cbcb05cda3ed/dqc_reference
[2023-07-01 00:24:03,429] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 00:24:03,430] [INFO] Task started: Prodigal
[2023-07-01 00:24:03,430] [INFO] Running command: gunzip -c /var/lib/cwl/stgdba5e395-4713-4f0f-ad77-da8fc6583a7b/GCA_016190535.1_ASM1619053v1_genomic.fna.gz | prodigal -d GCA_016190535.1_ASM1619053v1_genomic.fna/cds.fna -a GCA_016190535.1_ASM1619053v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 00:24:05,580] [INFO] Task succeeded: Prodigal
[2023-07-01 00:24:05,581] [INFO] Task started: HMMsearch
[2023-07-01 00:24:05,581] [INFO] Running command: hmmsearch --tblout GCA_016190535.1_ASM1619053v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg683f455f-c027-4441-9d1b-cbcb05cda3ed/dqc_reference/reference_markers.hmm GCA_016190535.1_ASM1619053v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 00:24:05,772] [INFO] Task succeeded: HMMsearch
[2023-07-01 00:24:05,774] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgdba5e395-4713-4f0f-ad77-da8fc6583a7b/GCA_016190535.1_ASM1619053v1_genomic.fna.gz]
[2023-07-01 00:24:05,789] [INFO] Query marker FASTA was written to GCA_016190535.1_ASM1619053v1_genomic.fna/markers.fasta
[2023-07-01 00:24:05,790] [INFO] Task started: Blastn
[2023-07-01 00:24:05,790] [INFO] Running command: blastn -query GCA_016190535.1_ASM1619053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg683f455f-c027-4441-9d1b-cbcb05cda3ed/dqc_reference/reference_markers.fasta -out GCA_016190535.1_ASM1619053v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:24:07,866] [INFO] Task succeeded: Blastn
[2023-07-01 00:24:07,870] [INFO] Selected 15 target genomes.
[2023-07-01 00:24:07,871] [INFO] Target genome list was writen to GCA_016190535.1_ASM1619053v1_genomic.fna/target_genomes.txt
[2023-07-01 00:24:07,872] [INFO] Task started: fastANI
[2023-07-01 00:24:07,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba5e395-4713-4f0f-ad77-da8fc6583a7b/GCA_016190535.1_ASM1619053v1_genomic.fna.gz --refList GCA_016190535.1_ASM1619053v1_genomic.fna/target_genomes.txt --output GCA_016190535.1_ASM1619053v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 00:24:14,858] [INFO] Task succeeded: fastANI
[2023-07-01 00:24:14,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg683f455f-c027-4441-9d1b-cbcb05cda3ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 00:24:14,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg683f455f-c027-4441-9d1b-cbcb05cda3ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 00:24:14,860] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 00:24:14,860] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 00:24:14,860] [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
--------------------------------------------------------------------------------
[2023-07-01 00:24:14,862] [INFO] DFAST Taxonomy check result was written to GCA_016190535.1_ASM1619053v1_genomic.fna/tc_result.tsv
[2023-07-01 00:24:14,863] [INFO] ===== Taxonomy check completed =====
[2023-07-01 00:24:14,863] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 00:24:14,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg683f455f-c027-4441-9d1b-cbcb05cda3ed/dqc_reference/checkm_data
[2023-07-01 00:24:14,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 00:24:14,881] [INFO] Task started: CheckM
[2023-07-01 00:24:14,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016190535.1_ASM1619053v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016190535.1_ASM1619053v1_genomic.fna/checkm_input GCA_016190535.1_ASM1619053v1_genomic.fna/checkm_result
[2023-07-01 00:24:29,223] [INFO] Task succeeded: CheckM
[2023-07-01 00:24:29,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.08%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 00:24:29,246] [INFO] ===== Completeness check finished =====
[2023-07-01 00:24:29,246] [INFO] ===== Start GTDB Search =====
[2023-07-01 00:24:29,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016190535.1_ASM1619053v1_genomic.fna/markers.fasta)
[2023-07-01 00:24:29,247] [INFO] Task started: Blastn
[2023-07-01 00:24:29,247] [INFO] Running command: blastn -query GCA_016190535.1_ASM1619053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg683f455f-c027-4441-9d1b-cbcb05cda3ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_016190535.1_ASM1619053v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:24:29,863] [INFO] Task succeeded: Blastn
[2023-07-01 00:24:29,868] [INFO] Selected 13 target genomes.
[2023-07-01 00:24:29,869] [INFO] Target genome list was writen to GCA_016190535.1_ASM1619053v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 00:24:29,876] [INFO] Task started: fastANI
[2023-07-01 00:24:29,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba5e395-4713-4f0f-ad77-da8fc6583a7b/GCA_016190535.1_ASM1619053v1_genomic.fna.gz --refList GCA_016190535.1_ASM1619053v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016190535.1_ASM1619053v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 00:24:34,952] [INFO] Task succeeded: fastANI
[2023-07-01 00:24:34,958] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 00:24:34,958] [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_016190535.1	s__JACPQK01 sp016190535	100.0	237	237	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__JACPQK01;f__JACPQK01;g__JACPQK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016190505.1	s__JACPQM01 sp016190505	77.8527	95	237	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__JACPQK01;f__JACPQK01;g__JACPQM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 00:24:34,961] [INFO] GTDB search result was written to GCA_016190535.1_ASM1619053v1_genomic.fna/result_gtdb.tsv
[2023-07-01 00:24:34,961] [INFO] ===== GTDB Search completed =====
[2023-07-01 00:24:34,963] [INFO] DFAST_QC result json was written to GCA_016190535.1_ASM1619053v1_genomic.fna/dqc_result.json
[2023-07-01 00:24:34,964] [INFO] DFAST_QC completed!
[2023-07-01 00:24:34,964] [INFO] Total running time: 0h0m34s