[2023-06-28 10:00:55,262] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:00:55,285] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:00:55,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg295cc4c2-82a2-432c-a370-9ccc4dedb687/dqc_reference
[2023-06-28 10:00:56,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:00:56,574] [INFO] Task started: Prodigal
[2023-06-28 10:00:56,574] [INFO] Running command: gunzip -c /var/lib/cwl/stg573ab774-ca0a-475a-86ff-2a2aa4076221/GCA_017533485.1_ASM1753348v1_genomic.fna.gz | prodigal -d GCA_017533485.1_ASM1753348v1_genomic.fna/cds.fna -a GCA_017533485.1_ASM1753348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:01:02,154] [INFO] Task succeeded: Prodigal
[2023-06-28 10:01:02,155] [INFO] Task started: HMMsearch
[2023-06-28 10:01:02,155] [INFO] Running command: hmmsearch --tblout GCA_017533485.1_ASM1753348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg295cc4c2-82a2-432c-a370-9ccc4dedb687/dqc_reference/reference_markers.hmm GCA_017533485.1_ASM1753348v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:01:02,446] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:01:02,450] [INFO] Found 6/6 markers.
[2023-06-28 10:01:02,497] [INFO] Query marker FASTA was written to GCA_017533485.1_ASM1753348v1_genomic.fna/markers.fasta
[2023-06-28 10:01:02,498] [INFO] Task started: Blastn
[2023-06-28 10:01:02,498] [INFO] Running command: blastn -query GCA_017533485.1_ASM1753348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg295cc4c2-82a2-432c-a370-9ccc4dedb687/dqc_reference/reference_markers.fasta -out GCA_017533485.1_ASM1753348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:01:03,207] [INFO] Task succeeded: Blastn
[2023-06-28 10:01:03,210] [INFO] Selected 22 target genomes.
[2023-06-28 10:01:03,211] [INFO] Target genome list was writen to GCA_017533485.1_ASM1753348v1_genomic.fna/target_genomes.txt
[2023-06-28 10:01:03,213] [INFO] Task started: fastANI
[2023-06-28 10:01:03,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg573ab774-ca0a-475a-86ff-2a2aa4076221/GCA_017533485.1_ASM1753348v1_genomic.fna.gz --refList GCA_017533485.1_ASM1753348v1_genomic.fna/target_genomes.txt --output GCA_017533485.1_ASM1753348v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:01:19,219] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:19,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg295cc4c2-82a2-432c-a370-9ccc4dedb687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:01:19,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg295cc4c2-82a2-432c-a370-9ccc4dedb687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:01:19,222] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:01:19,222] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:01:19,222] [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 10:01:19,224] [INFO] DFAST Taxonomy check result was written to GCA_017533485.1_ASM1753348v1_genomic.fna/tc_result.tsv
[2023-06-28 10:01:19,225] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:01:19,225] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:01:19,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg295cc4c2-82a2-432c-a370-9ccc4dedb687/dqc_reference/checkm_data
[2023-06-28 10:01:19,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:01:19,251] [INFO] Task started: CheckM
[2023-06-28 10:01:19,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017533485.1_ASM1753348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017533485.1_ASM1753348v1_genomic.fna/checkm_input GCA_017533485.1_ASM1753348v1_genomic.fna/checkm_result
[2023-06-28 10:01:43,588] [INFO] Task succeeded: CheckM
[2023-06-28 10:01:43,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:01:43,613] [INFO] ===== Completeness check finished =====
[2023-06-28 10:01:43,613] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:01:43,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017533485.1_ASM1753348v1_genomic.fna/markers.fasta)
[2023-06-28 10:01:43,614] [INFO] Task started: Blastn
[2023-06-28 10:01:43,614] [INFO] Running command: blastn -query GCA_017533485.1_ASM1753348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg295cc4c2-82a2-432c-a370-9ccc4dedb687/dqc_reference/reference_markers_gtdb.fasta -out GCA_017533485.1_ASM1753348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:01:44,658] [INFO] Task succeeded: Blastn
[2023-06-28 10:01:44,662] [INFO] Selected 14 target genomes.
[2023-06-28 10:01:44,663] [INFO] Target genome list was writen to GCA_017533485.1_ASM1753348v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:01:44,665] [INFO] Task started: fastANI
[2023-06-28 10:01:44,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg573ab774-ca0a-475a-86ff-2a2aa4076221/GCA_017533485.1_ASM1753348v1_genomic.fna.gz --refList GCA_017533485.1_ASM1753348v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017533485.1_ASM1753348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:01:53,879] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:53,896] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:01:53,897] [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_017533485.1	s__Firm-04 sp017533485	100.0	661	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001603005.1	s__Firm-04 sp001603005	77.5474	135	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	97.77	97.77	0.85	0.85	2	-
GCA_017523995.1	s__Firm-04 sp017523995	77.4932	132	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427265.1	s__Firm-04 sp017427265	77.2501	153	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291435.1	s__Firm-04 sp016291435	77.243	121	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	97.69	97.69	0.87	0.87	2	-
GCA_016296505.1	s__Firm-04 sp016296505	77.189	130	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001940925.1	s__Firm-04 sp001940925	77.1844	135	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	95.65	95.65	0.68	0.68	2	-
GCA_017545185.1	s__Firm-04 sp017545185	77.1508	124	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066805.1	s__Firm-04 sp015066805	77.093	109	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395085.1	s__Firm-04 sp002395085	77.0424	123	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017532085.1	s__Firm-04 sp017532085	76.9235	105	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016281125.1	s__Firm-04 sp016281125	76.8716	144	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	95.42	95.42	0.98	0.98	2	-
GCA_017541275.1	s__Firm-04 sp017541275	76.7769	105	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018110935.1	s__Firm-04 sp018110935	76.6658	71	666	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:01:53,899] [INFO] GTDB search result was written to GCA_017533485.1_ASM1753348v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:01:53,900] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:01:53,904] [INFO] DFAST_QC result json was written to GCA_017533485.1_ASM1753348v1_genomic.fna/dqc_result.json
[2023-06-28 10:01:53,904] [INFO] DFAST_QC completed!
[2023-06-28 10:01:53,904] [INFO] Total running time: 0h0m59s