[2023-06-29 08:24:17,707] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:24:17,724] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:24:17,724] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8ab764f-1034-474b-9366-bdb4461023c9/dqc_reference
[2023-06-29 08:24:20,051] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:24:20,052] [INFO] Task started: Prodigal
[2023-06-29 08:24:20,053] [INFO] Running command: gunzip -c /var/lib/cwl/stgce314547-dd63-4324-ad35-9b669592f4d8/GCA_020721345.1_ASM2072134v1_genomic.fna.gz | prodigal -d GCA_020721345.1_ASM2072134v1_genomic.fna/cds.fna -a GCA_020721345.1_ASM2072134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:24:22,463] [INFO] Task succeeded: Prodigal
[2023-06-29 08:24:22,464] [INFO] Task started: HMMsearch
[2023-06-29 08:24:22,464] [INFO] Running command: hmmsearch --tblout GCA_020721345.1_ASM2072134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8ab764f-1034-474b-9366-bdb4461023c9/dqc_reference/reference_markers.hmm GCA_020721345.1_ASM2072134v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:24:22,677] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:24:22,679] [INFO] Found 6/6 markers.
[2023-06-29 08:24:22,703] [INFO] Query marker FASTA was written to GCA_020721345.1_ASM2072134v1_genomic.fna/markers.fasta
[2023-06-29 08:24:22,703] [INFO] Task started: Blastn
[2023-06-29 08:24:22,703] [INFO] Running command: blastn -query GCA_020721345.1_ASM2072134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8ab764f-1034-474b-9366-bdb4461023c9/dqc_reference/reference_markers.fasta -out GCA_020721345.1_ASM2072134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:24:23,967] [INFO] Task succeeded: Blastn
[2023-06-29 08:24:23,971] [INFO] Selected 19 target genomes.
[2023-06-29 08:24:23,972] [INFO] Target genome list was writen to GCA_020721345.1_ASM2072134v1_genomic.fna/target_genomes.txt
[2023-06-29 08:24:23,978] [INFO] Task started: fastANI
[2023-06-29 08:24:23,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgce314547-dd63-4324-ad35-9b669592f4d8/GCA_020721345.1_ASM2072134v1_genomic.fna.gz --refList GCA_020721345.1_ASM2072134v1_genomic.fna/target_genomes.txt --output GCA_020721345.1_ASM2072134v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:24:31,813] [INFO] Task succeeded: fastANI
[2023-06-29 08:24:31,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8ab764f-1034-474b-9366-bdb4461023c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:24:31,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8ab764f-1034-474b-9366-bdb4461023c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:24:31,817] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:24:31,817] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 08:24:31,817] [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
--------------------------------------------------------------------------------
[2023-06-29 08:24:31,819] [INFO] DFAST Taxonomy check result was written to GCA_020721345.1_ASM2072134v1_genomic.fna/tc_result.tsv
[2023-06-29 08:24:31,820] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:24:31,820] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:24:31,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8ab764f-1034-474b-9366-bdb4461023c9/dqc_reference/checkm_data
[2023-06-29 08:24:31,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:24:31,841] [INFO] Task started: CheckM
[2023-06-29 08:24:31,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020721345.1_ASM2072134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020721345.1_ASM2072134v1_genomic.fna/checkm_input GCA_020721345.1_ASM2072134v1_genomic.fna/checkm_result
[2023-06-29 08:24:47,707] [INFO] Task succeeded: CheckM
[2023-06-29 08:24:47,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:24:47,738] [INFO] ===== Completeness check finished =====
[2023-06-29 08:24:47,738] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:24:47,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020721345.1_ASM2072134v1_genomic.fna/markers.fasta)
[2023-06-29 08:24:47,739] [INFO] Task started: Blastn
[2023-06-29 08:24:47,739] [INFO] Running command: blastn -query GCA_020721345.1_ASM2072134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8ab764f-1034-474b-9366-bdb4461023c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_020721345.1_ASM2072134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:24:48,582] [INFO] Task succeeded: Blastn
[2023-06-29 08:24:48,601] [INFO] Selected 22 target genomes.
[2023-06-29 08:24:48,601] [INFO] Target genome list was writen to GCA_020721345.1_ASM2072134v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:24:48,615] [INFO] Task started: fastANI
[2023-06-29 08:24:48,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgce314547-dd63-4324-ad35-9b669592f4d8/GCA_020721345.1_ASM2072134v1_genomic.fna.gz --refList GCA_020721345.1_ASM2072134v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020721345.1_ASM2072134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:24:55,228] [INFO] Task succeeded: fastANI
[2023-06-29 08:24:55,238] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:24:55,239] [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_001493195.1	s__BN30871 sp001493195	81.2617	285	389	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__BN30871	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002424475.1	s__BN30871 sp002424475	77.4612	115	389	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__BN30871	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937075.1	s__BN30871 sp016937075	77.0736	91	389	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__BN30871	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002412865.1	s__BN30871 sp002412865	77.0158	64	389	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__BN30871	95.0	99.84	99.84	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 08:24:55,241] [INFO] GTDB search result was written to GCA_020721345.1_ASM2072134v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:24:55,241] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:24:55,244] [INFO] DFAST_QC result json was written to GCA_020721345.1_ASM2072134v1_genomic.fna/dqc_result.json
[2023-06-29 08:24:55,244] [INFO] DFAST_QC completed!
[2023-06-29 08:24:55,244] [INFO] Total running time: 0h0m38s