[2023-06-27 01:35:42,251] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:35:42,253] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:35:42,253] [INFO] DQC Reference Directory: /var/lib/cwl/stgf18e0bed-b1de-426b-b599-1a5b8768d488/dqc_reference
[2023-06-27 01:35:43,451] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:35:43,452] [INFO] Task started: Prodigal
[2023-06-27 01:35:43,452] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaa80aec-4151-419f-915b-8411a0e8e3f9/GCA_002310215.1_ASM231021v1_genomic.fna.gz | prodigal -d GCA_002310215.1_ASM231021v1_genomic.fna/cds.fna -a GCA_002310215.1_ASM231021v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:36:05,297] [INFO] Task succeeded: Prodigal
[2023-06-27 01:36:05,298] [INFO] Task started: HMMsearch
[2023-06-27 01:36:05,298] [INFO] Running command: hmmsearch --tblout GCA_002310215.1_ASM231021v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf18e0bed-b1de-426b-b599-1a5b8768d488/dqc_reference/reference_markers.hmm GCA_002310215.1_ASM231021v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:36:05,582] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:36:05,584] [INFO] Found 6/6 markers.
[2023-06-27 01:36:05,615] [INFO] Query marker FASTA was written to GCA_002310215.1_ASM231021v1_genomic.fna/markers.fasta
[2023-06-27 01:36:05,616] [INFO] Task started: Blastn
[2023-06-27 01:36:05,616] [INFO] Running command: blastn -query GCA_002310215.1_ASM231021v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf18e0bed-b1de-426b-b599-1a5b8768d488/dqc_reference/reference_markers.fasta -out GCA_002310215.1_ASM231021v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:36:06,214] [INFO] Task succeeded: Blastn
[2023-06-27 01:36:06,219] [INFO] Selected 24 target genomes.
[2023-06-27 01:36:06,219] [INFO] Target genome list was writen to GCA_002310215.1_ASM231021v1_genomic.fna/target_genomes.txt
[2023-06-27 01:36:06,221] [INFO] Task started: fastANI
[2023-06-27 01:36:06,221] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaa80aec-4151-419f-915b-8411a0e8e3f9/GCA_002310215.1_ASM231021v1_genomic.fna.gz --refList GCA_002310215.1_ASM231021v1_genomic.fna/target_genomes.txt --output GCA_002310215.1_ASM231021v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 01:36:20,401] [INFO] Task succeeded: fastANI
[2023-06-27 01:36:20,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf18e0bed-b1de-426b-b599-1a5b8768d488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 01:36:20,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf18e0bed-b1de-426b-b599-1a5b8768d488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 01:36:20,404] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 01:36:20,405] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 01:36:20,405] [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
--------------------------------------------------------------------------------
[2023-06-27 01:36:20,407] [INFO] DFAST Taxonomy check result was written to GCA_002310215.1_ASM231021v1_genomic.fna/tc_result.tsv
[2023-06-27 01:36:20,408] [INFO] ===== Taxonomy check completed =====
[2023-06-27 01:36:20,408] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:36:20,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf18e0bed-b1de-426b-b599-1a5b8768d488/dqc_reference/checkm_data
[2023-06-27 01:36:20,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:36:20,470] [INFO] Task started: CheckM
[2023-06-27 01:36:20,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310215.1_ASM231021v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310215.1_ASM231021v1_genomic.fna/checkm_input GCA_002310215.1_ASM231021v1_genomic.fna/checkm_result
[2023-06-27 01:37:22,932] [INFO] Task succeeded: CheckM
[2023-06-27 01:37:22,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:37:22,955] [INFO] ===== Completeness check finished =====
[2023-06-27 01:37:22,955] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:37:22,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310215.1_ASM231021v1_genomic.fna/markers.fasta)
[2023-06-27 01:37:22,956] [INFO] Task started: Blastn
[2023-06-27 01:37:22,956] [INFO] Running command: blastn -query GCA_002310215.1_ASM231021v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf18e0bed-b1de-426b-b599-1a5b8768d488/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310215.1_ASM231021v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:37:23,806] [INFO] Task succeeded: Blastn
[2023-06-27 01:37:23,811] [INFO] Selected 6 target genomes.
[2023-06-27 01:37:23,811] [INFO] Target genome list was writen to GCA_002310215.1_ASM231021v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:37:23,817] [INFO] Task started: fastANI
[2023-06-27 01:37:23,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaa80aec-4151-419f-915b-8411a0e8e3f9/GCA_002310215.1_ASM231021v1_genomic.fna.gz --refList GCA_002310215.1_ASM231021v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310215.1_ASM231021v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:37:28,887] [INFO] Task succeeded: fastANI
[2023-06-27 01:37:28,895] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 01:37:28,896] [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_002310215.1	s__UBA1181 sp002310215	100.0	1117	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	98.50	97.06	0.94	0.92	3	conclusive
GCA_016285885.1	s__UBA1181 sp016285885	91.8178	897	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017649635.1	s__UBA1181 sp017649635	89.0589	603	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017527905.1	s__UBA1181 sp017527905	88.5964	760	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962085.1	s__UBA1181 sp017962085	88.1105	804	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	98.52	98.52	0.88	0.88	2	-
GCA_017550335.1	s__UBA1181 sp017550335	87.8207	781	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA1181	95.0	96.84	96.79	0.92	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-27 01:37:28,899] [INFO] GTDB search result was written to GCA_002310215.1_ASM231021v1_genomic.fna/result_gtdb.tsv
[2023-06-27 01:37:28,900] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:37:28,902] [INFO] DFAST_QC result json was written to GCA_002310215.1_ASM231021v1_genomic.fna/dqc_result.json
[2023-06-27 01:37:28,902] [INFO] DFAST_QC completed!
[2023-06-27 01:37:28,903] [INFO] Total running time: 0h1m47s