[2023-06-28 18:45:48,908] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:45:48,910] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:45:48,911] [INFO] DQC Reference Directory: /var/lib/cwl/stge3b1bf9c-bcf0-43de-babb-16d8cd8f54a3/dqc_reference
[2023-06-28 18:45:50,146] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:45:50,146] [INFO] Task started: Prodigal
[2023-06-28 18:45:50,147] [INFO] Running command: gunzip -c /var/lib/cwl/stg8808066c-07a7-47b2-827e-425e9ef29815/GCA_015231995.1_ASM1523199v1_genomic.fna.gz | prodigal -d GCA_015231995.1_ASM1523199v1_genomic.fna/cds.fna -a GCA_015231995.1_ASM1523199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:45:57,939] [INFO] Task succeeded: Prodigal
[2023-06-28 18:45:57,939] [INFO] Task started: HMMsearch
[2023-06-28 18:45:57,940] [INFO] Running command: hmmsearch --tblout GCA_015231995.1_ASM1523199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3b1bf9c-bcf0-43de-babb-16d8cd8f54a3/dqc_reference/reference_markers.hmm GCA_015231995.1_ASM1523199v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:45:58,195] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:45:58,196] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8808066c-07a7-47b2-827e-425e9ef29815/GCA_015231995.1_ASM1523199v1_genomic.fna.gz]
[2023-06-28 18:45:58,229] [INFO] Query marker FASTA was written to GCA_015231995.1_ASM1523199v1_genomic.fna/markers.fasta
[2023-06-28 18:45:58,229] [INFO] Task started: Blastn
[2023-06-28 18:45:58,229] [INFO] Running command: blastn -query GCA_015231995.1_ASM1523199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3b1bf9c-bcf0-43de-babb-16d8cd8f54a3/dqc_reference/reference_markers.fasta -out GCA_015231995.1_ASM1523199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:45:58,848] [INFO] Task succeeded: Blastn
[2023-06-28 18:45:58,853] [INFO] Selected 30 target genomes.
[2023-06-28 18:45:58,854] [INFO] Target genome list was writen to GCA_015231995.1_ASM1523199v1_genomic.fna/target_genomes.txt
[2023-06-28 18:45:58,855] [INFO] Task started: fastANI
[2023-06-28 18:45:58,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg8808066c-07a7-47b2-827e-425e9ef29815/GCA_015231995.1_ASM1523199v1_genomic.fna.gz --refList GCA_015231995.1_ASM1523199v1_genomic.fna/target_genomes.txt --output GCA_015231995.1_ASM1523199v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:46:20,012] [INFO] Task succeeded: fastANI
[2023-06-28 18:46:20,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3b1bf9c-bcf0-43de-babb-16d8cd8f54a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:46:20,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3b1bf9c-bcf0-43de-babb-16d8cd8f54a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:46:20,015] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:46:20,015] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:46:20,015] [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 18:46:20,017] [INFO] DFAST Taxonomy check result was written to GCA_015231995.1_ASM1523199v1_genomic.fna/tc_result.tsv
[2023-06-28 18:46:20,018] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:46:20,018] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:46:20,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3b1bf9c-bcf0-43de-babb-16d8cd8f54a3/dqc_reference/checkm_data
[2023-06-28 18:46:20,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:46:20,058] [INFO] Task started: CheckM
[2023-06-28 18:46:20,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015231995.1_ASM1523199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015231995.1_ASM1523199v1_genomic.fna/checkm_input GCA_015231995.1_ASM1523199v1_genomic.fna/checkm_result
[2023-06-28 18:46:48,137] [INFO] Task succeeded: CheckM
[2023-06-28 18:46:48,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:46:48,168] [INFO] ===== Completeness check finished =====
[2023-06-28 18:46:48,168] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:46:48,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015231995.1_ASM1523199v1_genomic.fna/markers.fasta)
[2023-06-28 18:46:48,169] [INFO] Task started: Blastn
[2023-06-28 18:46:48,170] [INFO] Running command: blastn -query GCA_015231995.1_ASM1523199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3b1bf9c-bcf0-43de-babb-16d8cd8f54a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_015231995.1_ASM1523199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:46:49,129] [INFO] Task succeeded: Blastn
[2023-06-28 18:46:49,134] [INFO] Selected 23 target genomes.
[2023-06-28 18:46:49,135] [INFO] Target genome list was writen to GCA_015231995.1_ASM1523199v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:46:49,145] [INFO] Task started: fastANI
[2023-06-28 18:46:49,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg8808066c-07a7-47b2-827e-425e9ef29815/GCA_015231995.1_ASM1523199v1_genomic.fna.gz --refList GCA_015231995.1_ASM1523199v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015231995.1_ASM1523199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:47:04,146] [INFO] Task succeeded: fastANI
[2023-06-28 18:47:04,154] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:47:04,154] [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_015231995.1	s__JADGAO01 sp015231995	99.9842	871	894	d__Bacteria;p__Nitrospinota;c__UBA7883;o__UBA7883;f__JACRLM01;g__JADGAO01	95.0	98.75	98.75	0.82	0.82	2	conclusive
GCA_016208975.1	s__JACQXA01 sp016208975	76.9723	112	894	d__Bacteria;p__Nitrospinota;c__UBA7883;o__UBA7883;f__JACRLM01;g__JACQXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235255.1	s__JACRLM01 sp016235255	76.4678	126	894	d__Bacteria;p__Nitrospinota;c__UBA7883;o__UBA7883;f__JACRLM01;g__JACRLM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:47:04,156] [INFO] GTDB search result was written to GCA_015231995.1_ASM1523199v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:47:04,157] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:47:04,159] [INFO] DFAST_QC result json was written to GCA_015231995.1_ASM1523199v1_genomic.fna/dqc_result.json
[2023-06-28 18:47:04,159] [INFO] DFAST_QC completed!
[2023-06-28 18:47:04,159] [INFO] Total running time: 0h1m15s