[2023-06-17 02:02:02,873] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:02:02,878] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:02:02,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg783f857b-fdd7-407f-b789-baea4573956b/dqc_reference
[2023-06-17 02:02:06,663] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:02:06,664] [INFO] Task started: Prodigal
[2023-06-17 02:02:06,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg664ad42d-a1aa-4362-8617-522953f56c7a/GCA_028818705.1_ASM2881870v1_genomic.fna.gz | prodigal -d GCA_028818705.1_ASM2881870v1_genomic.fna/cds.fna -a GCA_028818705.1_ASM2881870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:02:21,581] [INFO] Task succeeded: Prodigal
[2023-06-17 02:02:21,581] [INFO] Task started: HMMsearch
[2023-06-17 02:02:21,582] [INFO] Running command: hmmsearch --tblout GCA_028818705.1_ASM2881870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg783f857b-fdd7-407f-b789-baea4573956b/dqc_reference/reference_markers.hmm GCA_028818705.1_ASM2881870v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:02:21,902] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:02:21,903] [INFO] Found 6/6 markers.
[2023-06-17 02:02:21,979] [INFO] Query marker FASTA was written to GCA_028818705.1_ASM2881870v1_genomic.fna/markers.fasta
[2023-06-17 02:02:21,980] [INFO] Task started: Blastn
[2023-06-17 02:02:21,980] [INFO] Running command: blastn -query GCA_028818705.1_ASM2881870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783f857b-fdd7-407f-b789-baea4573956b/dqc_reference/reference_markers.fasta -out GCA_028818705.1_ASM2881870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:02:22,542] [INFO] Task succeeded: Blastn
[2023-06-17 02:02:22,546] [INFO] Selected 4 target genomes.
[2023-06-17 02:02:22,546] [INFO] Target genome list was writen to GCA_028818705.1_ASM2881870v1_genomic.fna/target_genomes.txt
[2023-06-17 02:02:22,548] [INFO] Task started: fastANI
[2023-06-17 02:02:22,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg664ad42d-a1aa-4362-8617-522953f56c7a/GCA_028818705.1_ASM2881870v1_genomic.fna.gz --refList GCA_028818705.1_ASM2881870v1_genomic.fna/target_genomes.txt --output GCA_028818705.1_ASM2881870v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:02:25,344] [INFO] Task succeeded: fastANI
[2023-06-17 02:02:25,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg783f857b-fdd7-407f-b789-baea4573956b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:02:25,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg783f857b-fdd7-407f-b789-baea4573956b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:02:25,348] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:02:25,348] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 02:02:25,348] [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
--------------------------------------------------------------------------------
[2023-06-17 02:02:25,350] [INFO] DFAST Taxonomy check result was written to GCA_028818705.1_ASM2881870v1_genomic.fna/tc_result.tsv
[2023-06-17 02:02:25,351] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:02:25,351] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:02:25,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg783f857b-fdd7-407f-b789-baea4573956b/dqc_reference/checkm_data
[2023-06-17 02:02:25,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:02:25,424] [INFO] Task started: CheckM
[2023-06-17 02:02:25,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028818705.1_ASM2881870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028818705.1_ASM2881870v1_genomic.fna/checkm_input GCA_028818705.1_ASM2881870v1_genomic.fna/checkm_result
[2023-06-17 02:03:12,594] [INFO] Task succeeded: CheckM
[2023-06-17 02:03:12,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:03:12,619] [INFO] ===== Completeness check finished =====
[2023-06-17 02:03:12,619] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:03:12,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028818705.1_ASM2881870v1_genomic.fna/markers.fasta)
[2023-06-17 02:03:12,620] [INFO] Task started: Blastn
[2023-06-17 02:03:12,620] [INFO] Running command: blastn -query GCA_028818705.1_ASM2881870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783f857b-fdd7-407f-b789-baea4573956b/dqc_reference/reference_markers_gtdb.fasta -out GCA_028818705.1_ASM2881870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:03:13,325] [INFO] Task succeeded: Blastn
[2023-06-17 02:03:13,330] [INFO] Selected 15 target genomes.
[2023-06-17 02:03:13,330] [INFO] Target genome list was writen to GCA_028818705.1_ASM2881870v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:03:13,338] [INFO] Task started: fastANI
[2023-06-17 02:03:13,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg664ad42d-a1aa-4362-8617-522953f56c7a/GCA_028818705.1_ASM2881870v1_genomic.fna.gz --refList GCA_028818705.1_ASM2881870v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028818705.1_ASM2881870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:03:27,661] [INFO] Task succeeded: fastANI
[2023-06-17 02:03:27,675] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 02:03:27,676] [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_009845505.1	s__VXZL01 sp009845505	80.6675	930	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__VXZL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843785.1	s__WGA-3G sp009843785	80.2765	836	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	99.87	99.87	0.97	0.97	3	-
GCA_009845545.1	s__WGA-3G sp009845545	79.318	789	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	99.90	99.90	0.93	0.93	2	-
GCA_003635195.1	s__WGA-3G sp003635195	79.1027	818	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009835515.1	s__WGA-3G sp009835515	78.8325	601	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	98.95	98.95	0.75	0.75	2	-
GCA_009841255.1	s__WGA-3G sp009841255	78.7453	912	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012271015.1	s__WGA-3G sp012271015	78.7207	746	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270875.1	s__WGA-3G sp012270875	78.5746	731	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003635255.1	s__WGA-3G sp003635255	78.4065	733	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571305.1	s__WGA-3G sp007571305	78.1994	773	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000406005.1	s__WGA-3G sp000406005	78.089	664	1896	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 02:03:27,678] [INFO] GTDB search result was written to GCA_028818705.1_ASM2881870v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:03:27,678] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:03:27,681] [INFO] DFAST_QC result json was written to GCA_028818705.1_ASM2881870v1_genomic.fna/dqc_result.json
[2023-06-17 02:03:27,682] [INFO] DFAST_QC completed!
[2023-06-17 02:03:27,682] [INFO] Total running time: 0h1m25s