[2023-06-18 11:25:12,689] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:25:12,691] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:25:12,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f4bd6aa-a7cb-408b-b19f-ad3c249774ff/dqc_reference
[2023-06-18 11:25:14,182] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:25:14,183] [INFO] Task started: Prodigal
[2023-06-18 11:25:14,183] [INFO] Running command: gunzip -c /var/lib/cwl/stgc662a170-d266-416b-97d9-a0cf80da8011/GCA_018652185.1_ASM1865218v1_genomic.fna.gz | prodigal -d GCA_018652185.1_ASM1865218v1_genomic.fna/cds.fna -a GCA_018652185.1_ASM1865218v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:25:16,850] [INFO] Task succeeded: Prodigal
[2023-06-18 11:25:16,850] [INFO] Task started: HMMsearch
[2023-06-18 11:25:16,850] [INFO] Running command: hmmsearch --tblout GCA_018652185.1_ASM1865218v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f4bd6aa-a7cb-408b-b19f-ad3c249774ff/dqc_reference/reference_markers.hmm GCA_018652185.1_ASM1865218v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:25:17,052] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:25:17,053] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc662a170-d266-416b-97d9-a0cf80da8011/GCA_018652185.1_ASM1865218v1_genomic.fna.gz]
[2023-06-18 11:25:17,079] [INFO] Query marker FASTA was written to GCA_018652185.1_ASM1865218v1_genomic.fna/markers.fasta
[2023-06-18 11:25:17,080] [INFO] Task started: Blastn
[2023-06-18 11:25:17,080] [INFO] Running command: blastn -query GCA_018652185.1_ASM1865218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f4bd6aa-a7cb-408b-b19f-ad3c249774ff/dqc_reference/reference_markers.fasta -out GCA_018652185.1_ASM1865218v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:25:19,784] [INFO] Task succeeded: Blastn
[2023-06-18 11:25:19,789] [INFO] Selected 5 target genomes.
[2023-06-18 11:25:19,789] [INFO] Target genome list was writen to GCA_018652185.1_ASM1865218v1_genomic.fna/target_genomes.txt
[2023-06-18 11:25:19,792] [INFO] Task started: fastANI
[2023-06-18 11:25:19,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgc662a170-d266-416b-97d9-a0cf80da8011/GCA_018652185.1_ASM1865218v1_genomic.fna.gz --refList GCA_018652185.1_ASM1865218v1_genomic.fna/target_genomes.txt --output GCA_018652185.1_ASM1865218v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:25:21,507] [INFO] Task succeeded: fastANI
[2023-06-18 11:25:21,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f4bd6aa-a7cb-408b-b19f-ad3c249774ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:25:21,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f4bd6aa-a7cb-408b-b19f-ad3c249774ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:25:21,510] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:25:21,510] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 11:25:21,510] [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 11:25:21,512] [INFO] DFAST Taxonomy check result was written to GCA_018652185.1_ASM1865218v1_genomic.fna/tc_result.tsv
[2023-06-18 11:25:21,513] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:25:21,513] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:25:21,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f4bd6aa-a7cb-408b-b19f-ad3c249774ff/dqc_reference/checkm_data
[2023-06-18 11:25:21,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:25:21,528] [INFO] Task started: CheckM
[2023-06-18 11:25:21,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018652185.1_ASM1865218v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018652185.1_ASM1865218v1_genomic.fna/checkm_input GCA_018652185.1_ASM1865218v1_genomic.fna/checkm_result
[2023-06-18 11:25:39,943] [INFO] Task succeeded: CheckM
[2023-06-18 11:25:39,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:25:39,972] [INFO] ===== Completeness check finished =====
[2023-06-18 11:25:39,973] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:25:39,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018652185.1_ASM1865218v1_genomic.fna/markers.fasta)
[2023-06-18 11:25:39,974] [INFO] Task started: Blastn
[2023-06-18 11:25:39,974] [INFO] Running command: blastn -query GCA_018652185.1_ASM1865218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f4bd6aa-a7cb-408b-b19f-ad3c249774ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_018652185.1_ASM1865218v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:25:40,690] [INFO] Task succeeded: Blastn
[2023-06-18 11:25:40,697] [INFO] Selected 8 target genomes.
[2023-06-18 11:25:40,698] [INFO] Target genome list was writen to GCA_018652185.1_ASM1865218v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:25:40,705] [INFO] Task started: fastANI
[2023-06-18 11:25:40,705] [INFO] Running command: fastANI --query /var/lib/cwl/stgc662a170-d266-416b-97d9-a0cf80da8011/GCA_018652185.1_ASM1865218v1_genomic.fna.gz --refList GCA_018652185.1_ASM1865218v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018652185.1_ASM1865218v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:25:42,358] [INFO] Task succeeded: fastANI
[2023-06-18 11:25:42,363] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:25:42,363] [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_018653485.1	s__JABIDS01 sp018653485	99.9992	307	308	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JABIDS01	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCA_017609795.1	s__JAFCDM01 sp017609795	77.3057	63	308	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAFCDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018304045.1	s__CABMGE01 sp018304045	76.8581	52	308	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__CABMGE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:25:42,365] [INFO] GTDB search result was written to GCA_018652185.1_ASM1865218v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:25:42,365] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:25:42,368] [INFO] DFAST_QC result json was written to GCA_018652185.1_ASM1865218v1_genomic.fna/dqc_result.json
[2023-06-18 11:25:42,369] [INFO] DFAST_QC completed!
[2023-06-18 11:25:42,369] [INFO] Total running time: 0h0m30s