[2023-06-28 14:18:55,677] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:18:55,680] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:18:55,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b90d44d-0964-444a-9389-4110a0d4c978/dqc_reference
[2023-06-28 14:18:56,923] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:18:56,924] [INFO] Task started: Prodigal
[2023-06-28 14:18:56,924] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb4b7717-f035-4b34-8c6d-866306af827e/GCA_002708085.1_ASM270808v1_genomic.fna.gz | prodigal -d GCA_002708085.1_ASM270808v1_genomic.fna/cds.fna -a GCA_002708085.1_ASM270808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:18:58,040] [INFO] Task succeeded: Prodigal
[2023-06-28 14:18:58,041] [INFO] Task started: HMMsearch
[2023-06-28 14:18:58,041] [INFO] Running command: hmmsearch --tblout GCA_002708085.1_ASM270808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b90d44d-0964-444a-9389-4110a0d4c978/dqc_reference/reference_markers.hmm GCA_002708085.1_ASM270808v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:18:58,156] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:18:58,157] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgfb4b7717-f035-4b34-8c6d-866306af827e/GCA_002708085.1_ASM270808v1_genomic.fna.gz]
[2023-06-28 14:18:58,169] [INFO] Query marker FASTA was written to GCA_002708085.1_ASM270808v1_genomic.fna/markers.fasta
[2023-06-28 14:18:58,170] [INFO] Task started: Blastn
[2023-06-28 14:18:58,170] [INFO] Running command: blastn -query GCA_002708085.1_ASM270808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b90d44d-0964-444a-9389-4110a0d4c978/dqc_reference/reference_markers.fasta -out GCA_002708085.1_ASM270808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:18:58,668] [INFO] Task succeeded: Blastn
[2023-06-28 14:18:58,672] [INFO] Selected 9 target genomes.
[2023-06-28 14:18:58,673] [INFO] Target genome list was writen to GCA_002708085.1_ASM270808v1_genomic.fna/target_genomes.txt
[2023-06-28 14:18:58,674] [INFO] Task started: fastANI
[2023-06-28 14:18:58,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb4b7717-f035-4b34-8c6d-866306af827e/GCA_002708085.1_ASM270808v1_genomic.fna.gz --refList GCA_002708085.1_ASM270808v1_genomic.fna/target_genomes.txt --output GCA_002708085.1_ASM270808v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:19:02,205] [INFO] Task succeeded: fastANI
[2023-06-28 14:19:02,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b90d44d-0964-444a-9389-4110a0d4c978/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:19:02,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b90d44d-0964-444a-9389-4110a0d4c978/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:19:02,208] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:19:02,208] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 14:19:02,208] [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
--------------------------------------------------------------------------------
[2023-06-28 14:19:02,211] [INFO] DFAST Taxonomy check result was written to GCA_002708085.1_ASM270808v1_genomic.fna/tc_result.tsv
[2023-06-28 14:19:02,212] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:19:02,212] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:19:02,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b90d44d-0964-444a-9389-4110a0d4c978/dqc_reference/checkm_data
[2023-06-28 14:19:02,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:19:02,230] [INFO] Task started: CheckM
[2023-06-28 14:19:02,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708085.1_ASM270808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708085.1_ASM270808v1_genomic.fna/checkm_input GCA_002708085.1_ASM270808v1_genomic.fna/checkm_result
[2023-06-28 14:19:12,967] [INFO] Task succeeded: CheckM
[2023-06-28 14:19:12,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:19:12,988] [INFO] ===== Completeness check finished =====
[2023-06-28 14:19:12,989] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:19:12,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708085.1_ASM270808v1_genomic.fna/markers.fasta)
[2023-06-28 14:19:12,989] [INFO] Task started: Blastn
[2023-06-28 14:19:12,989] [INFO] Running command: blastn -query GCA_002708085.1_ASM270808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b90d44d-0964-444a-9389-4110a0d4c978/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708085.1_ASM270808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:19:13,521] [INFO] Task succeeded: Blastn
[2023-06-28 14:19:13,525] [INFO] Selected 8 target genomes.
[2023-06-28 14:19:13,525] [INFO] Target genome list was writen to GCA_002708085.1_ASM270808v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:19:13,527] [INFO] Task started: fastANI
[2023-06-28 14:19:13,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb4b7717-f035-4b34-8c6d-866306af827e/GCA_002708085.1_ASM270808v1_genomic.fna.gz --refList GCA_002708085.1_ASM270808v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708085.1_ASM270808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:19:15,607] [INFO] Task succeeded: fastANI
[2023-06-28 14:19:15,611] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:19:15,611] [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_002708085.1	s__GCA-2721615 sp002708085	100.0	220	221	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-2721615	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002721615.1	s__GCA-2721615 sp002721615	89.0748	197	221	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-2721615	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:19:15,613] [INFO] GTDB search result was written to GCA_002708085.1_ASM270808v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:19:15,614] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:19:15,616] [INFO] DFAST_QC result json was written to GCA_002708085.1_ASM270808v1_genomic.fna/dqc_result.json
[2023-06-28 14:19:15,617] [INFO] DFAST_QC completed!
[2023-06-28 14:19:15,617] [INFO] Total running time: 0h0m20s