[2023-06-28 04:20:20,415] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:20:20,418] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:20:20,418] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7822677-871f-4b2c-88cc-55ffe2784fa4/dqc_reference
[2023-06-28 04:20:21,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:20:21,766] [INFO] Task started: Prodigal
[2023-06-28 04:20:21,767] [INFO] Running command: gunzip -c /var/lib/cwl/stge7db4d78-5c47-4a59-8338-c86e3e83b57b/GCA_017482585.1_ASM1748258v1_genomic.fna.gz | prodigal -d GCA_017482585.1_ASM1748258v1_genomic.fna/cds.fna -a GCA_017482585.1_ASM1748258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:20:27,731] [INFO] Task succeeded: Prodigal
[2023-06-28 04:20:27,731] [INFO] Task started: HMMsearch
[2023-06-28 04:20:27,731] [INFO] Running command: hmmsearch --tblout GCA_017482585.1_ASM1748258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7822677-871f-4b2c-88cc-55ffe2784fa4/dqc_reference/reference_markers.hmm GCA_017482585.1_ASM1748258v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:20:27,966] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:20:27,967] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge7db4d78-5c47-4a59-8338-c86e3e83b57b/GCA_017482585.1_ASM1748258v1_genomic.fna.gz]
[2023-06-28 04:20:27,999] [INFO] Query marker FASTA was written to GCA_017482585.1_ASM1748258v1_genomic.fna/markers.fasta
[2023-06-28 04:20:28,000] [INFO] Task started: Blastn
[2023-06-28 04:20:28,000] [INFO] Running command: blastn -query GCA_017482585.1_ASM1748258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7822677-871f-4b2c-88cc-55ffe2784fa4/dqc_reference/reference_markers.fasta -out GCA_017482585.1_ASM1748258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:20:28,599] [INFO] Task succeeded: Blastn
[2023-06-28 04:20:28,609] [INFO] Selected 24 target genomes.
[2023-06-28 04:20:28,610] [INFO] Target genome list was writen to GCA_017482585.1_ASM1748258v1_genomic.fna/target_genomes.txt
[2023-06-28 04:20:28,611] [INFO] Task started: fastANI
[2023-06-28 04:20:28,611] [INFO] Running command: fastANI --query /var/lib/cwl/stge7db4d78-5c47-4a59-8338-c86e3e83b57b/GCA_017482585.1_ASM1748258v1_genomic.fna.gz --refList GCA_017482585.1_ASM1748258v1_genomic.fna/target_genomes.txt --output GCA_017482585.1_ASM1748258v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:20:53,068] [INFO] Task succeeded: fastANI
[2023-06-28 04:20:53,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7822677-871f-4b2c-88cc-55ffe2784fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:20:53,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7822677-871f-4b2c-88cc-55ffe2784fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:20:53,071] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:20:53,071] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:20:53,071] [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 04:20:53,074] [INFO] DFAST Taxonomy check result was written to GCA_017482585.1_ASM1748258v1_genomic.fna/tc_result.tsv
[2023-06-28 04:20:53,075] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:20:53,075] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:20:53,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7822677-871f-4b2c-88cc-55ffe2784fa4/dqc_reference/checkm_data
[2023-06-28 04:20:53,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:20:53,123] [INFO] Task started: CheckM
[2023-06-28 04:20:53,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017482585.1_ASM1748258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017482585.1_ASM1748258v1_genomic.fna/checkm_input GCA_017482585.1_ASM1748258v1_genomic.fna/checkm_result
[2023-06-28 04:21:16,571] [INFO] Task succeeded: CheckM
[2023-06-28 04:21:16,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 5.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-28 04:21:16,600] [INFO] ===== Completeness check finished =====
[2023-06-28 04:21:16,600] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:21:16,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017482585.1_ASM1748258v1_genomic.fna/markers.fasta)
[2023-06-28 04:21:16,601] [INFO] Task started: Blastn
[2023-06-28 04:21:16,601] [INFO] Running command: blastn -query GCA_017482585.1_ASM1748258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7822677-871f-4b2c-88cc-55ffe2784fa4/dqc_reference/reference_markers_gtdb.fasta -out GCA_017482585.1_ASM1748258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:21:17,342] [INFO] Task succeeded: Blastn
[2023-06-28 04:21:17,347] [INFO] Selected 7 target genomes.
[2023-06-28 04:21:17,347] [INFO] Target genome list was writen to GCA_017482585.1_ASM1748258v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:21:17,351] [INFO] Task started: fastANI
[2023-06-28 04:21:17,351] [INFO] Running command: fastANI --query /var/lib/cwl/stge7db4d78-5c47-4a59-8338-c86e3e83b57b/GCA_017482585.1_ASM1748258v1_genomic.fna.gz --refList GCA_017482585.1_ASM1748258v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017482585.1_ASM1748258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:21:22,020] [INFO] Task succeeded: fastANI
[2023-06-28 04:21:22,032] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 04:21:22,033] [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_017937485.1	s__RUG369 sp017937485	93.3018	473	511	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937685.1	s__RUG369 sp017937685	91.9828	451	511	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436025.1	s__RUG369 sp017436025	91.7316	449	511	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435375.1	s__RUG369 sp017435375	91.0052	412	511	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017466305.1	s__RUG369 sp017466305	90.7162	358	511	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017559825.1	s__RUG369 sp017559825	89.2718	438	511	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549085.1	s__RUG369 sp017549085	88.2088	304	511	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG369	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 04:21:22,035] [INFO] GTDB search result was written to GCA_017482585.1_ASM1748258v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:21:22,036] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:21:22,039] [INFO] DFAST_QC result json was written to GCA_017482585.1_ASM1748258v1_genomic.fna/dqc_result.json
[2023-06-28 04:21:22,040] [INFO] DFAST_QC completed!
[2023-06-28 04:21:22,040] [INFO] Total running time: 0h1m2s