[2023-06-18 23:17:33,735] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:17:33,738] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:17:33,738] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0fad4bf-5ffd-4d27-8832-e9a68da48228/dqc_reference
[2023-06-18 23:17:35,141] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:17:35,141] [INFO] Task started: Prodigal
[2023-06-18 23:17:35,142] [INFO] Running command: gunzip -c /var/lib/cwl/stg376192e5-f58d-47c9-acb9-3ce3e9ec7f70/GCA_018697955.1_ASM1869795v1_genomic.fna.gz | prodigal -d GCA_018697955.1_ASM1869795v1_genomic.fna/cds.fna -a GCA_018697955.1_ASM1869795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:17:38,121] [INFO] Task succeeded: Prodigal
[2023-06-18 23:17:38,122] [INFO] Task started: HMMsearch
[2023-06-18 23:17:38,122] [INFO] Running command: hmmsearch --tblout GCA_018697955.1_ASM1869795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0fad4bf-5ffd-4d27-8832-e9a68da48228/dqc_reference/reference_markers.hmm GCA_018697955.1_ASM1869795v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:17:38,370] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:17:38,372] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg376192e5-f58d-47c9-acb9-3ce3e9ec7f70/GCA_018697955.1_ASM1869795v1_genomic.fna.gz]
[2023-06-18 23:17:38,394] [INFO] Query marker FASTA was written to GCA_018697955.1_ASM1869795v1_genomic.fna/markers.fasta
[2023-06-18 23:17:38,394] [INFO] Task started: Blastn
[2023-06-18 23:17:38,394] [INFO] Running command: blastn -query GCA_018697955.1_ASM1869795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0fad4bf-5ffd-4d27-8832-e9a68da48228/dqc_reference/reference_markers.fasta -out GCA_018697955.1_ASM1869795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:17:38,997] [INFO] Task succeeded: Blastn
[2023-06-18 23:17:39,001] [INFO] Selected 18 target genomes.
[2023-06-18 23:17:39,002] [INFO] Target genome list was writen to GCA_018697955.1_ASM1869795v1_genomic.fna/target_genomes.txt
[2023-06-18 23:17:39,006] [INFO] Task started: fastANI
[2023-06-18 23:17:39,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg376192e5-f58d-47c9-acb9-3ce3e9ec7f70/GCA_018697955.1_ASM1869795v1_genomic.fna.gz --refList GCA_018697955.1_ASM1869795v1_genomic.fna/target_genomes.txt --output GCA_018697955.1_ASM1869795v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:17:50,327] [INFO] Task succeeded: fastANI
[2023-06-18 23:17:50,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0fad4bf-5ffd-4d27-8832-e9a68da48228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:17:50,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0fad4bf-5ffd-4d27-8832-e9a68da48228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:17:50,330] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:17:50,330] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 23:17:50,330] [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
--------------------------------------------------------------------------------
[2023-06-18 23:17:50,332] [INFO] DFAST Taxonomy check result was written to GCA_018697955.1_ASM1869795v1_genomic.fna/tc_result.tsv
[2023-06-18 23:17:50,333] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:17:50,333] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:17:50,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0fad4bf-5ffd-4d27-8832-e9a68da48228/dqc_reference/checkm_data
[2023-06-18 23:17:50,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:17:50,383] [INFO] Task started: CheckM
[2023-06-18 23:17:50,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018697955.1_ASM1869795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018697955.1_ASM1869795v1_genomic.fna/checkm_input GCA_018697955.1_ASM1869795v1_genomic.fna/checkm_result
[2023-06-18 23:18:08,533] [INFO] Task succeeded: CheckM
[2023-06-18 23:18:08,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.92%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:18:08,555] [INFO] ===== Completeness check finished =====
[2023-06-18 23:18:08,556] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:18:08,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018697955.1_ASM1869795v1_genomic.fna/markers.fasta)
[2023-06-18 23:18:08,557] [INFO] Task started: Blastn
[2023-06-18 23:18:08,557] [INFO] Running command: blastn -query GCA_018697955.1_ASM1869795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0fad4bf-5ffd-4d27-8832-e9a68da48228/dqc_reference/reference_markers_gtdb.fasta -out GCA_018697955.1_ASM1869795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:18:09,430] [INFO] Task succeeded: Blastn
[2023-06-18 23:18:09,434] [INFO] Selected 15 target genomes.
[2023-06-18 23:18:09,434] [INFO] Target genome list was writen to GCA_018697955.1_ASM1869795v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:18:09,441] [INFO] Task started: fastANI
[2023-06-18 23:18:09,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg376192e5-f58d-47c9-acb9-3ce3e9ec7f70/GCA_018697955.1_ASM1869795v1_genomic.fna.gz --refList GCA_018697955.1_ASM1869795v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018697955.1_ASM1869795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:18:15,763] [INFO] Task succeeded: fastANI
[2023-06-18 23:18:15,769] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:18:15,769] [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_018647025.1	s__Nitromaritima sp018647025	98.2619	279	456	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	98.38	98.13	0.71	0.67	3	conclusive
GCA_000372225.1	s__Nitromaritima sp000372225	82.1353	260	456	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018697205.1	s__Nitromaritima sp018697205	80.0568	285	456	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	99.64	99.64	0.83	0.83	2	-
GCA_905182935.1	s__Nitromaritima sp905182935	77.7962	109	456	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 23:18:15,771] [INFO] GTDB search result was written to GCA_018697955.1_ASM1869795v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:18:15,772] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:18:15,774] [INFO] DFAST_QC result json was written to GCA_018697955.1_ASM1869795v1_genomic.fna/dqc_result.json
[2023-06-18 23:18:15,774] [INFO] DFAST_QC completed!
[2023-06-18 23:18:15,775] [INFO] Total running time: 0h0m42s