[2023-06-28 06:25:51,499] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:25:51,501] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:25:51,501] [INFO] DQC Reference Directory: /var/lib/cwl/stgf62e2834-7c1a-4f4e-a39f-726c5c835adb/dqc_reference
[2023-06-28 06:25:52,809] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:25:52,810] [INFO] Task started: Prodigal
[2023-06-28 06:25:52,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b139181-afd5-4611-ba04-20e2fc040cf7/GCA_017445585.1_ASM1744558v1_genomic.fna.gz | prodigal -d GCA_017445585.1_ASM1744558v1_genomic.fna/cds.fna -a GCA_017445585.1_ASM1744558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:25:58,544] [INFO] Task succeeded: Prodigal
[2023-06-28 06:25:58,545] [INFO] Task started: HMMsearch
[2023-06-28 06:25:58,545] [INFO] Running command: hmmsearch --tblout GCA_017445585.1_ASM1744558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf62e2834-7c1a-4f4e-a39f-726c5c835adb/dqc_reference/reference_markers.hmm GCA_017445585.1_ASM1744558v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:25:58,792] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:25:58,794] [INFO] Found 6/6 markers.
[2023-06-28 06:25:58,819] [INFO] Query marker FASTA was written to GCA_017445585.1_ASM1744558v1_genomic.fna/markers.fasta
[2023-06-28 06:25:58,819] [INFO] Task started: Blastn
[2023-06-28 06:25:58,820] [INFO] Running command: blastn -query GCA_017445585.1_ASM1744558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf62e2834-7c1a-4f4e-a39f-726c5c835adb/dqc_reference/reference_markers.fasta -out GCA_017445585.1_ASM1744558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:25:59,418] [INFO] Task succeeded: Blastn
[2023-06-28 06:25:59,423] [INFO] Selected 20 target genomes.
[2023-06-28 06:25:59,423] [INFO] Target genome list was writen to GCA_017445585.1_ASM1744558v1_genomic.fna/target_genomes.txt
[2023-06-28 06:25:59,426] [INFO] Task started: fastANI
[2023-06-28 06:25:59,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b139181-afd5-4611-ba04-20e2fc040cf7/GCA_017445585.1_ASM1744558v1_genomic.fna.gz --refList GCA_017445585.1_ASM1744558v1_genomic.fna/target_genomes.txt --output GCA_017445585.1_ASM1744558v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:26:09,677] [INFO] Task succeeded: fastANI
[2023-06-28 06:26:09,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf62e2834-7c1a-4f4e-a39f-726c5c835adb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:26:09,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf62e2834-7c1a-4f4e-a39f-726c5c835adb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:26:09,680] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:26:09,680] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 06:26:09,681] [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 06:26:09,683] [INFO] DFAST Taxonomy check result was written to GCA_017445585.1_ASM1744558v1_genomic.fna/tc_result.tsv
[2023-06-28 06:26:09,684] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:26:09,684] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:26:09,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf62e2834-7c1a-4f4e-a39f-726c5c835adb/dqc_reference/checkm_data
[2023-06-28 06:26:09,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:26:09,716] [INFO] Task started: CheckM
[2023-06-28 06:26:09,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017445585.1_ASM1744558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017445585.1_ASM1744558v1_genomic.fna/checkm_input GCA_017445585.1_ASM1744558v1_genomic.fna/checkm_result
[2023-06-28 06:26:33,580] [INFO] Task succeeded: CheckM
[2023-06-28 06:26:33,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 06:26:33,609] [INFO] ===== Completeness check finished =====
[2023-06-28 06:26:33,609] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:26:33,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017445585.1_ASM1744558v1_genomic.fna/markers.fasta)
[2023-06-28 06:26:33,610] [INFO] Task started: Blastn
[2023-06-28 06:26:33,610] [INFO] Running command: blastn -query GCA_017445585.1_ASM1744558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf62e2834-7c1a-4f4e-a39f-726c5c835adb/dqc_reference/reference_markers_gtdb.fasta -out GCA_017445585.1_ASM1744558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:26:34,498] [INFO] Task succeeded: Blastn
[2023-06-28 06:26:34,505] [INFO] Selected 24 target genomes.
[2023-06-28 06:26:34,506] [INFO] Target genome list was writen to GCA_017445585.1_ASM1744558v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:26:34,517] [INFO] Task started: fastANI
[2023-06-28 06:26:34,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b139181-afd5-4611-ba04-20e2fc040cf7/GCA_017445585.1_ASM1744558v1_genomic.fna.gz --refList GCA_017445585.1_ASM1744558v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017445585.1_ASM1744558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:26:44,919] [INFO] Task succeeded: fastANI
[2023-06-28 06:26:44,926] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:26:44,926] [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_017445585.1	s__UBA3774 sp017445585	100.0	767	772	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3774	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017455435.1	s__UBA3774 sp017455435	77.3839	68	772	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3774	95.0	97.91	97.91	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-28 06:26:44,928] [INFO] GTDB search result was written to GCA_017445585.1_ASM1744558v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:26:44,929] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:26:44,932] [INFO] DFAST_QC result json was written to GCA_017445585.1_ASM1744558v1_genomic.fna/dqc_result.json
[2023-06-28 06:26:44,933] [INFO] DFAST_QC completed!
[2023-06-28 06:26:44,933] [INFO] Total running time: 0h0m53s