[2023-06-13 04:35:52,409] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:35:52,410] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:35:52,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c3aa148-f8ca-42de-ac1b-4f9cfeb87233/dqc_reference
[2023-06-13 04:35:56,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:35:56,078] [INFO] Task started: Prodigal
[2023-06-13 04:35:56,079] [INFO] Running command: gunzip -c /var/lib/cwl/stgadf0500c-e1ae-4ff9-9484-0cdd5e62cf97/GCA_003545535.1_ASM354553v1_genomic.fna.gz | prodigal -d GCA_003545535.1_ASM354553v1_genomic.fna/cds.fna -a GCA_003545535.1_ASM354553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:36:00,740] [INFO] Task succeeded: Prodigal
[2023-06-13 04:36:00,740] [INFO] Task started: HMMsearch
[2023-06-13 04:36:00,740] [INFO] Running command: hmmsearch --tblout GCA_003545535.1_ASM354553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c3aa148-f8ca-42de-ac1b-4f9cfeb87233/dqc_reference/reference_markers.hmm GCA_003545535.1_ASM354553v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:36:00,934] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:36:00,936] [INFO] Found 6/6 markers.
[2023-06-13 04:36:00,964] [INFO] Query marker FASTA was written to GCA_003545535.1_ASM354553v1_genomic.fna/markers.fasta
[2023-06-13 04:36:00,964] [INFO] Task started: Blastn
[2023-06-13 04:36:00,964] [INFO] Running command: blastn -query GCA_003545535.1_ASM354553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c3aa148-f8ca-42de-ac1b-4f9cfeb87233/dqc_reference/reference_markers.fasta -out GCA_003545535.1_ASM354553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:01,643] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:01,669] [INFO] Selected 13 target genomes.
[2023-06-13 04:36:01,670] [INFO] Target genome list was writen to GCA_003545535.1_ASM354553v1_genomic.fna/target_genomes.txt
[2023-06-13 04:36:01,683] [INFO] Task started: fastANI
[2023-06-13 04:36:01,683] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf0500c-e1ae-4ff9-9484-0cdd5e62cf97/GCA_003545535.1_ASM354553v1_genomic.fna.gz --refList GCA_003545535.1_ASM354553v1_genomic.fna/target_genomes.txt --output GCA_003545535.1_ASM354553v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:36:07,943] [INFO] Task succeeded: fastANI
[2023-06-13 04:36:07,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c3aa148-f8ca-42de-ac1b-4f9cfeb87233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:36:07,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c3aa148-f8ca-42de-ac1b-4f9cfeb87233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:36:07,946] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:36:07,947] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 04:36:07,947] [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
--------------------------------------------------------------------------------
[2023-06-13 04:36:07,958] [INFO] DFAST Taxonomy check result was written to GCA_003545535.1_ASM354553v1_genomic.fna/tc_result.tsv
[2023-06-13 04:36:07,959] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:36:07,960] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:36:07,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c3aa148-f8ca-42de-ac1b-4f9cfeb87233/dqc_reference/checkm_data
[2023-06-13 04:36:07,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:36:07,991] [INFO] Task started: CheckM
[2023-06-13 04:36:07,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003545535.1_ASM354553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003545535.1_ASM354553v1_genomic.fna/checkm_input GCA_003545535.1_ASM354553v1_genomic.fna/checkm_result
[2023-06-13 04:36:29,694] [INFO] Task succeeded: CheckM
[2023-06-13 04:36:29,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 3.70%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-13 04:36:29,725] [INFO] ===== Completeness check finished =====
[2023-06-13 04:36:29,725] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:36:29,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003545535.1_ASM354553v1_genomic.fna/markers.fasta)
[2023-06-13 04:36:29,726] [INFO] Task started: Blastn
[2023-06-13 04:36:29,726] [INFO] Running command: blastn -query GCA_003545535.1_ASM354553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c3aa148-f8ca-42de-ac1b-4f9cfeb87233/dqc_reference/reference_markers_gtdb.fasta -out GCA_003545535.1_ASM354553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:30,617] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:30,622] [INFO] Selected 18 target genomes.
[2023-06-13 04:36:30,622] [INFO] Target genome list was writen to GCA_003545535.1_ASM354553v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:36:30,641] [INFO] Task started: fastANI
[2023-06-13 04:36:30,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf0500c-e1ae-4ff9-9484-0cdd5e62cf97/GCA_003545535.1_ASM354553v1_genomic.fna.gz --refList GCA_003545535.1_ASM354553v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003545535.1_ASM354553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:36:37,319] [INFO] Task succeeded: fastANI
[2023-06-13 04:36:37,325] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 04:36:37,326] [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_001825035.1	s__UBA10102 sp001825035	99.9167	213	223	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Paceibacterales;f__UBA10102;g__UBA10102	95.0	99.93	99.87	0.96	0.96	12	conclusive
GCA_016181405.1	s__O2-01-FULL-48-27b sp016181405	80.8418	54	223	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Paceibacterales;f__UBA10102;g__O2-01-FULL-48-27b	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 04:36:37,332] [INFO] GTDB search result was written to GCA_003545535.1_ASM354553v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:36:37,333] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:36:37,338] [INFO] DFAST_QC result json was written to GCA_003545535.1_ASM354553v1_genomic.fna/dqc_result.json
[2023-06-13 04:36:37,338] [INFO] DFAST_QC completed!
[2023-06-13 04:36:37,339] [INFO] Total running time: 0h0m45s