[2023-06-19 13:14:06,463] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:14:06,466] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:14:06,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d203052-db5e-4776-bea6-ba65345088ad/dqc_reference
[2023-06-19 13:14:07,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:14:07,843] [INFO] Task started: Prodigal
[2023-06-19 13:14:07,843] [INFO] Running command: gunzip -c /var/lib/cwl/stgea74491f-84e7-454c-84eb-5ac37feb0e52/GCA_013002425.1_ASM1300242v1_genomic.fna.gz | prodigal -d GCA_013002425.1_ASM1300242v1_genomic.fna/cds.fna -a GCA_013002425.1_ASM1300242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:14:15,847] [INFO] Task succeeded: Prodigal
[2023-06-19 13:14:15,848] [INFO] Task started: HMMsearch
[2023-06-19 13:14:15,848] [INFO] Running command: hmmsearch --tblout GCA_013002425.1_ASM1300242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d203052-db5e-4776-bea6-ba65345088ad/dqc_reference/reference_markers.hmm GCA_013002425.1_ASM1300242v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:14:16,128] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:14:16,130] [INFO] Found 6/6 markers.
[2023-06-19 13:14:16,169] [INFO] Query marker FASTA was written to GCA_013002425.1_ASM1300242v1_genomic.fna/markers.fasta
[2023-06-19 13:14:16,170] [INFO] Task started: Blastn
[2023-06-19 13:14:16,170] [INFO] Running command: blastn -query GCA_013002425.1_ASM1300242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d203052-db5e-4776-bea6-ba65345088ad/dqc_reference/reference_markers.fasta -out GCA_013002425.1_ASM1300242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:14:16,778] [INFO] Task succeeded: Blastn
[2023-06-19 13:14:16,784] [INFO] Selected 23 target genomes.
[2023-06-19 13:14:16,785] [INFO] Target genome list was writen to GCA_013002425.1_ASM1300242v1_genomic.fna/target_genomes.txt
[2023-06-19 13:14:16,791] [INFO] Task started: fastANI
[2023-06-19 13:14:16,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgea74491f-84e7-454c-84eb-5ac37feb0e52/GCA_013002425.1_ASM1300242v1_genomic.fna.gz --refList GCA_013002425.1_ASM1300242v1_genomic.fna/target_genomes.txt --output GCA_013002425.1_ASM1300242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:14:33,321] [INFO] Task succeeded: fastANI
[2023-06-19 13:14:33,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d203052-db5e-4776-bea6-ba65345088ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:14:33,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d203052-db5e-4776-bea6-ba65345088ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:14:33,323] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:14:33,323] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 13:14:33,323] [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
--------------------------------------------------------------------------------
[2023-06-19 13:14:33,326] [INFO] DFAST Taxonomy check result was written to GCA_013002425.1_ASM1300242v1_genomic.fna/tc_result.tsv
[2023-06-19 13:14:33,326] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:14:33,326] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:14:33,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d203052-db5e-4776-bea6-ba65345088ad/dqc_reference/checkm_data
[2023-06-19 13:14:33,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:14:33,369] [INFO] Task started: CheckM
[2023-06-19 13:14:33,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013002425.1_ASM1300242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013002425.1_ASM1300242v1_genomic.fna/checkm_input GCA_013002425.1_ASM1300242v1_genomic.fna/checkm_result
[2023-06-19 13:15:01,981] [INFO] Task succeeded: CheckM
[2023-06-19 13:15:01,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 7.70%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-19 13:15:02,014] [INFO] ===== Completeness check finished =====
[2023-06-19 13:15:02,014] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:15:02,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013002425.1_ASM1300242v1_genomic.fna/markers.fasta)
[2023-06-19 13:15:02,015] [INFO] Task started: Blastn
[2023-06-19 13:15:02,015] [INFO] Running command: blastn -query GCA_013002425.1_ASM1300242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d203052-db5e-4776-bea6-ba65345088ad/dqc_reference/reference_markers_gtdb.fasta -out GCA_013002425.1_ASM1300242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:15:02,875] [INFO] Task succeeded: Blastn
[2023-06-19 13:15:02,880] [INFO] Selected 19 target genomes.
[2023-06-19 13:15:02,880] [INFO] Target genome list was writen to GCA_013002425.1_ASM1300242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:15:02,889] [INFO] Task started: fastANI
[2023-06-19 13:15:02,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgea74491f-84e7-454c-84eb-5ac37feb0e52/GCA_013002425.1_ASM1300242v1_genomic.fna.gz --refList GCA_013002425.1_ASM1300242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013002425.1_ASM1300242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:15:15,624] [INFO] Task succeeded: fastANI
[2023-06-19 13:15:15,634] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:15:15,634] [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_013002425.1	s__JABDJQ01 sp013002425	100.0	848	860	d__Bacteria;p__JABDJQ01;c__JABDJQ01;o__JABDJQ01;f__JABDJQ01;g__JABDJQ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016867715.1	s__VGIW01 sp016867715	75.7808	65	860	d__Bacteria;p__JABDJQ01;c__JABDJQ01;o__JABDJQ01;f__JABDJQ01;g__VGIW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016930695.1	s__JAFGGD01 sp016930695	75.3642	53	860	d__Bacteria;p__JABDJQ01;c__JABDJQ01;o__JABDJQ01;f__JABDJQ01;g__JAFGGD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714045.1	s__JADJNY01 sp016714045	74.8719	55	860	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793095.1	s__JAEUJQ01 sp016793095	74.5329	59	860	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:15:15,636] [INFO] GTDB search result was written to GCA_013002425.1_ASM1300242v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:15:15,637] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:15:15,640] [INFO] DFAST_QC result json was written to GCA_013002425.1_ASM1300242v1_genomic.fna/dqc_result.json
[2023-06-19 13:15:15,640] [INFO] DFAST_QC completed!
[2023-06-19 13:15:15,641] [INFO] Total running time: 0h1m9s