[2023-06-28 17:50:18,274] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:50:18,276] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:50:18,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg3643d72a-b7ae-494f-b0a4-e5f626cde6da/dqc_reference
[2023-06-28 17:50:19,491] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:50:19,492] [INFO] Task started: Prodigal
[2023-06-28 17:50:19,492] [INFO] Running command: gunzip -c /var/lib/cwl/stg74a284fd-2d98-4140-8fd9-b19dafd9aaf3/GCA_015663935.1_ASM1566393v1_genomic.fna.gz | prodigal -d GCA_015663935.1_ASM1566393v1_genomic.fna/cds.fna -a GCA_015663935.1_ASM1566393v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:50:25,983] [INFO] Task succeeded: Prodigal
[2023-06-28 17:50:25,984] [INFO] Task started: HMMsearch
[2023-06-28 17:50:25,984] [INFO] Running command: hmmsearch --tblout GCA_015663935.1_ASM1566393v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3643d72a-b7ae-494f-b0a4-e5f626cde6da/dqc_reference/reference_markers.hmm GCA_015663935.1_ASM1566393v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:50:26,241] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:50:26,242] [INFO] Found 6/6 markers.
[2023-06-28 17:50:26,268] [INFO] Query marker FASTA was written to GCA_015663935.1_ASM1566393v1_genomic.fna/markers.fasta
[2023-06-28 17:50:26,268] [INFO] Task started: Blastn
[2023-06-28 17:50:26,268] [INFO] Running command: blastn -query GCA_015663935.1_ASM1566393v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3643d72a-b7ae-494f-b0a4-e5f626cde6da/dqc_reference/reference_markers.fasta -out GCA_015663935.1_ASM1566393v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:50:26,916] [INFO] Task succeeded: Blastn
[2023-06-28 17:50:26,922] [INFO] Selected 20 target genomes.
[2023-06-28 17:50:26,922] [INFO] Target genome list was writen to GCA_015663935.1_ASM1566393v1_genomic.fna/target_genomes.txt
[2023-06-28 17:50:26,928] [INFO] Task started: fastANI
[2023-06-28 17:50:26,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a284fd-2d98-4140-8fd9-b19dafd9aaf3/GCA_015663935.1_ASM1566393v1_genomic.fna.gz --refList GCA_015663935.1_ASM1566393v1_genomic.fna/target_genomes.txt --output GCA_015663935.1_ASM1566393v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:50:39,215] [INFO] Task succeeded: fastANI
[2023-06-28 17:50:39,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3643d72a-b7ae-494f-b0a4-e5f626cde6da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:50:39,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3643d72a-b7ae-494f-b0a4-e5f626cde6da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:50:39,219] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:50:39,219] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:50:39,219] [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 17:50:39,222] [INFO] DFAST Taxonomy check result was written to GCA_015663935.1_ASM1566393v1_genomic.fna/tc_result.tsv
[2023-06-28 17:50:39,223] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:50:39,223] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:50:39,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3643d72a-b7ae-494f-b0a4-e5f626cde6da/dqc_reference/checkm_data
[2023-06-28 17:50:39,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:50:39,260] [INFO] Task started: CheckM
[2023-06-28 17:50:39,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015663935.1_ASM1566393v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015663935.1_ASM1566393v1_genomic.fna/checkm_input GCA_015663935.1_ASM1566393v1_genomic.fna/checkm_result
[2023-06-28 17:51:04,707] [INFO] Task succeeded: CheckM
[2023-06-28 17:51:04,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:51:04,731] [INFO] ===== Completeness check finished =====
[2023-06-28 17:51:04,732] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:51:04,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015663935.1_ASM1566393v1_genomic.fna/markers.fasta)
[2023-06-28 17:51:04,732] [INFO] Task started: Blastn
[2023-06-28 17:51:04,733] [INFO] Running command: blastn -query GCA_015663935.1_ASM1566393v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3643d72a-b7ae-494f-b0a4-e5f626cde6da/dqc_reference/reference_markers_gtdb.fasta -out GCA_015663935.1_ASM1566393v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:51:05,783] [INFO] Task succeeded: Blastn
[2023-06-28 17:51:05,789] [INFO] Selected 12 target genomes.
[2023-06-28 17:51:05,789] [INFO] Target genome list was writen to GCA_015663935.1_ASM1566393v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:51:05,802] [INFO] Task started: fastANI
[2023-06-28 17:51:05,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a284fd-2d98-4140-8fd9-b19dafd9aaf3/GCA_015663935.1_ASM1566393v1_genomic.fna.gz --refList GCA_015663935.1_ASM1566393v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015663935.1_ASM1566393v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:51:12,433] [INFO] Task succeeded: fastANI
[2023-06-28 17:51:12,443] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:51:12,443] [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_003447825.1	s__REDSEA-S09-B13 sp003447825	99.3451	705	763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__REDSEA-S09-B13	95.0	99.33	99.08	0.90	0.86	16	conclusive
GCA_002731295.1	s__REDSEA-S09-B13 sp002731295	87.5065	514	763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__REDSEA-S09-B13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002456995.1	s__REDSEA-S09-B13 sp002456995	86.9795	359	763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__REDSEA-S09-B13	95.0	96.76	96.75	0.88	0.88	3	-
GCA_001629395.1	s__REDSEA-S09-B13 sp001629395	85.9103	504	763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__REDSEA-S09-B13	95.0	98.93	98.69	0.85	0.83	6	-
GCA_002718155.1	s__UBA9619 sp002718155	77.6321	84	763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA9619	95.0	99.32	99.28	0.82	0.80	3	-
--------------------------------------------------------------------------------
[2023-06-28 17:51:12,445] [INFO] GTDB search result was written to GCA_015663935.1_ASM1566393v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:51:12,446] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:51:12,449] [INFO] DFAST_QC result json was written to GCA_015663935.1_ASM1566393v1_genomic.fna/dqc_result.json
[2023-06-28 17:51:12,449] [INFO] DFAST_QC completed!
[2023-06-28 17:51:12,449] [INFO] Total running time: 0h0m54s