[2023-06-28 21:51:13,626] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:51:13,628] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:51:13,628] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb9af7d7-2f9b-435d-a74a-6ed67b20a3e4/dqc_reference
[2023-06-28 21:51:14,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:51:14,838] [INFO] Task started: Prodigal
[2023-06-28 21:51:14,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ec8ec29-ea35-4e46-a2c6-35c0dfc28ad1/GCA_020440385.1_ASM2044038v1_genomic.fna.gz | prodigal -d GCA_020440385.1_ASM2044038v1_genomic.fna/cds.fna -a GCA_020440385.1_ASM2044038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:51:19,165] [INFO] Task succeeded: Prodigal
[2023-06-28 21:51:19,165] [INFO] Task started: HMMsearch
[2023-06-28 21:51:19,166] [INFO] Running command: hmmsearch --tblout GCA_020440385.1_ASM2044038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb9af7d7-2f9b-435d-a74a-6ed67b20a3e4/dqc_reference/reference_markers.hmm GCA_020440385.1_ASM2044038v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:51:19,401] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:51:19,403] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ec8ec29-ea35-4e46-a2c6-35c0dfc28ad1/GCA_020440385.1_ASM2044038v1_genomic.fna.gz]
[2023-06-28 21:51:19,432] [INFO] Query marker FASTA was written to GCA_020440385.1_ASM2044038v1_genomic.fna/markers.fasta
[2023-06-28 21:51:19,432] [INFO] Task started: Blastn
[2023-06-28 21:51:19,433] [INFO] Running command: blastn -query GCA_020440385.1_ASM2044038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb9af7d7-2f9b-435d-a74a-6ed67b20a3e4/dqc_reference/reference_markers.fasta -out GCA_020440385.1_ASM2044038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:51:20,106] [INFO] Task succeeded: Blastn
[2023-06-28 21:51:20,111] [INFO] Selected 15 target genomes.
[2023-06-28 21:51:20,111] [INFO] Target genome list was writen to GCA_020440385.1_ASM2044038v1_genomic.fna/target_genomes.txt
[2023-06-28 21:51:20,117] [INFO] Task started: fastANI
[2023-06-28 21:51:20,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ec8ec29-ea35-4e46-a2c6-35c0dfc28ad1/GCA_020440385.1_ASM2044038v1_genomic.fna.gz --refList GCA_020440385.1_ASM2044038v1_genomic.fna/target_genomes.txt --output GCA_020440385.1_ASM2044038v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:51:26,902] [INFO] Task succeeded: fastANI
[2023-06-28 21:51:26,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb9af7d7-2f9b-435d-a74a-6ed67b20a3e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:51:26,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb9af7d7-2f9b-435d-a74a-6ed67b20a3e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:51:26,906] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:51:26,906] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:51:26,906] [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 21:51:26,909] [INFO] DFAST Taxonomy check result was written to GCA_020440385.1_ASM2044038v1_genomic.fna/tc_result.tsv
[2023-06-28 21:51:26,910] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:51:26,910] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:51:26,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb9af7d7-2f9b-435d-a74a-6ed67b20a3e4/dqc_reference/checkm_data
[2023-06-28 21:51:26,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:51:26,944] [INFO] Task started: CheckM
[2023-06-28 21:51:26,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020440385.1_ASM2044038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020440385.1_ASM2044038v1_genomic.fna/checkm_input GCA_020440385.1_ASM2044038v1_genomic.fna/checkm_result
[2023-06-28 21:51:47,869] [INFO] Task succeeded: CheckM
[2023-06-28 21:51:47,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 9.32%
Strain heterogeneity: 14.29%
--------------------------------------------------------------------------------
[2023-06-28 21:51:47,898] [INFO] ===== Completeness check finished =====
[2023-06-28 21:51:47,899] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:51:47,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020440385.1_ASM2044038v1_genomic.fna/markers.fasta)
[2023-06-28 21:51:47,899] [INFO] Task started: Blastn
[2023-06-28 21:51:47,899] [INFO] Running command: blastn -query GCA_020440385.1_ASM2044038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb9af7d7-2f9b-435d-a74a-6ed67b20a3e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_020440385.1_ASM2044038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:51:48,611] [INFO] Task succeeded: Blastn
[2023-06-28 21:51:48,616] [INFO] Selected 26 target genomes.
[2023-06-28 21:51:48,616] [INFO] Target genome list was writen to GCA_020440385.1_ASM2044038v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:51:48,631] [INFO] Task started: fastANI
[2023-06-28 21:51:48,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ec8ec29-ea35-4e46-a2c6-35c0dfc28ad1/GCA_020440385.1_ASM2044038v1_genomic.fna.gz --refList GCA_020440385.1_ASM2044038v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020440385.1_ASM2044038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:51:55,911] [INFO] Task succeeded: fastANI
[2023-06-28 21:51:55,917] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 21:51:55,918] [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_018399075.1	s__Neptunochlamydia sp018399075	76.7513	72	497	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Simkaniaceae;g__Neptunochlamydia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356785.1	s__Neptunochlamydia vexilliferae	76.2115	60	497	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Simkaniaceae;g__Neptunochlamydia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:51:55,920] [INFO] GTDB search result was written to GCA_020440385.1_ASM2044038v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:51:55,921] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:51:55,923] [INFO] DFAST_QC result json was written to GCA_020440385.1_ASM2044038v1_genomic.fna/dqc_result.json
[2023-06-28 21:51:55,924] [INFO] DFAST_QC completed!
[2023-06-28 21:51:55,924] [INFO] Total running time: 0h0m42s