[2023-06-30 00:55:34,726] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:55:34,734] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:55:34,734] [INFO] DQC Reference Directory: /var/lib/cwl/stgf585ba98-13d4-4a6e-afa2-37edff6364ed/dqc_reference
[2023-06-30 00:55:36,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:55:36,103] [INFO] Task started: Prodigal
[2023-06-30 00:55:36,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1ad615a-3df7-488e-944b-31874a1ac8a6/GCA_024223955.1_ASM2422395v1_genomic.fna.gz | prodigal -d GCA_024223955.1_ASM2422395v1_genomic.fna/cds.fna -a GCA_024223955.1_ASM2422395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:55:57,885] [INFO] Task succeeded: Prodigal
[2023-06-30 00:55:57,885] [INFO] Task started: HMMsearch
[2023-06-30 00:55:57,885] [INFO] Running command: hmmsearch --tblout GCA_024223955.1_ASM2422395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf585ba98-13d4-4a6e-afa2-37edff6364ed/dqc_reference/reference_markers.hmm GCA_024223955.1_ASM2422395v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:55:58,382] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:55:58,384] [INFO] Found 6/6 markers.
[2023-06-30 00:55:58,458] [INFO] Query marker FASTA was written to GCA_024223955.1_ASM2422395v1_genomic.fna/markers.fasta
[2023-06-30 00:55:58,458] [INFO] Task started: Blastn
[2023-06-30 00:55:58,458] [INFO] Running command: blastn -query GCA_024223955.1_ASM2422395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf585ba98-13d4-4a6e-afa2-37edff6364ed/dqc_reference/reference_markers.fasta -out GCA_024223955.1_ASM2422395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:55:59,050] [INFO] Task succeeded: Blastn
[2023-06-30 00:55:59,054] [INFO] Selected 25 target genomes.
[2023-06-30 00:55:59,055] [INFO] Target genome list was writen to GCA_024223955.1_ASM2422395v1_genomic.fna/target_genomes.txt
[2023-06-30 00:55:59,057] [INFO] Task started: fastANI
[2023-06-30 00:55:59,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1ad615a-3df7-488e-944b-31874a1ac8a6/GCA_024223955.1_ASM2422395v1_genomic.fna.gz --refList GCA_024223955.1_ASM2422395v1_genomic.fna/target_genomes.txt --output GCA_024223955.1_ASM2422395v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:56:16,917] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:16,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf585ba98-13d4-4a6e-afa2-37edff6364ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:56:16,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf585ba98-13d4-4a6e-afa2-37edff6364ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:56:16,920] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:56:16,920] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:56:16,920] [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
--------------------------------------------------------------------------------
[2023-06-30 00:56:16,922] [INFO] DFAST Taxonomy check result was written to GCA_024223955.1_ASM2422395v1_genomic.fna/tc_result.tsv
[2023-06-30 00:56:16,923] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:56:16,923] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:56:16,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf585ba98-13d4-4a6e-afa2-37edff6364ed/dqc_reference/checkm_data
[2023-06-30 00:56:16,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:56:17,020] [INFO] Task started: CheckM
[2023-06-30 00:56:17,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024223955.1_ASM2422395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024223955.1_ASM2422395v1_genomic.fna/checkm_input GCA_024223955.1_ASM2422395v1_genomic.fna/checkm_result
[2023-06-30 00:57:22,633] [INFO] Task succeeded: CheckM
[2023-06-30 00:57:22,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 19.16%
Strain heterogeneity: 13.79%
--------------------------------------------------------------------------------
[2023-06-30 00:57:22,669] [INFO] ===== Completeness check finished =====
[2023-06-30 00:57:22,669] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:57:22,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024223955.1_ASM2422395v1_genomic.fna/markers.fasta)
[2023-06-30 00:57:22,670] [INFO] Task started: Blastn
[2023-06-30 00:57:22,670] [INFO] Running command: blastn -query GCA_024223955.1_ASM2422395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf585ba98-13d4-4a6e-afa2-37edff6364ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_024223955.1_ASM2422395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:57:23,433] [INFO] Task succeeded: Blastn
[2023-06-30 00:57:23,439] [INFO] Selected 21 target genomes.
[2023-06-30 00:57:23,439] [INFO] Target genome list was writen to GCA_024223955.1_ASM2422395v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:57:23,474] [INFO] Task started: fastANI
[2023-06-30 00:57:23,474] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1ad615a-3df7-488e-944b-31874a1ac8a6/GCA_024223955.1_ASM2422395v1_genomic.fna.gz --refList GCA_024223955.1_ASM2422395v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024223955.1_ASM2422395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:57:40,259] [INFO] Task succeeded: fastANI
[2023-06-30 00:57:40,271] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:57:40,272] [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_014384025.1	s__NIOZ-UU13 sp014384025	83.9374	1154	2688	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__NIOZ-UU13	95.0	99.70	99.70	0.88	0.88	2	-
GCA_013202635.1	s__NIOZ-UU13 sp013202635	83.4241	656	2688	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__NIOZ-UU13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016782865.1	s__SG8-4 sp016782865	77.7318	267	2688	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__SG8-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005223045.1	s__SG8-4 sp005223045	77.5521	314	2688	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__SG8-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003644295.1	s__B140-G9 sp003644295	76.8868	53	2688	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__B140-G9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349615.1	s__CS2-K091 sp013349615	76.2964	139	2688	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__CS2-K091	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016934255.1	s__JAFGPJ01 sp016934255	76.1325	107	2688	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__JAFGPJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931715.1	s__JAFGPS01 sp016931715	75.3987	58	2688	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__JAFGPS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:57:40,274] [INFO] GTDB search result was written to GCA_024223955.1_ASM2422395v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:57:40,274] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:57:40,277] [INFO] DFAST_QC result json was written to GCA_024223955.1_ASM2422395v1_genomic.fna/dqc_result.json
[2023-06-30 00:57:40,277] [INFO] DFAST_QC completed!
[2023-06-30 00:57:40,277] [INFO] Total running time: 0h2m6s