[2023-06-18 11:02:18,952] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:02:18,955] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:02:18,955] [INFO] DQC Reference Directory: /var/lib/cwl/stg65689e9e-733b-4137-973e-1474eff755b5/dqc_reference
[2023-06-18 11:02:20,348] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:02:20,349] [INFO] Task started: Prodigal
[2023-06-18 11:02:20,349] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfd4045d-3756-474e-a105-f0b811d82d4f/GCA_013697425.1_ASM1369742v1_genomic.fna.gz | prodigal -d GCA_013697425.1_ASM1369742v1_genomic.fna/cds.fna -a GCA_013697425.1_ASM1369742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:02:24,653] [INFO] Task succeeded: Prodigal
[2023-06-18 11:02:24,654] [INFO] Task started: HMMsearch
[2023-06-18 11:02:24,654] [INFO] Running command: hmmsearch --tblout GCA_013697425.1_ASM1369742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65689e9e-733b-4137-973e-1474eff755b5/dqc_reference/reference_markers.hmm GCA_013697425.1_ASM1369742v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:02:24,872] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:02:24,873] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbfd4045d-3756-474e-a105-f0b811d82d4f/GCA_013697425.1_ASM1369742v1_genomic.fna.gz]
[2023-06-18 11:02:24,905] [INFO] Query marker FASTA was written to GCA_013697425.1_ASM1369742v1_genomic.fna/markers.fasta
[2023-06-18 11:02:24,906] [INFO] Task started: Blastn
[2023-06-18 11:02:24,906] [INFO] Running command: blastn -query GCA_013697425.1_ASM1369742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65689e9e-733b-4137-973e-1474eff755b5/dqc_reference/reference_markers.fasta -out GCA_013697425.1_ASM1369742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:02:25,548] [INFO] Task succeeded: Blastn
[2023-06-18 11:02:25,555] [INFO] Selected 14 target genomes.
[2023-06-18 11:02:25,555] [INFO] Target genome list was writen to GCA_013697425.1_ASM1369742v1_genomic.fna/target_genomes.txt
[2023-06-18 11:02:25,560] [INFO] Task started: fastANI
[2023-06-18 11:02:25,560] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd4045d-3756-474e-a105-f0b811d82d4f/GCA_013697425.1_ASM1369742v1_genomic.fna.gz --refList GCA_013697425.1_ASM1369742v1_genomic.fna/target_genomes.txt --output GCA_013697425.1_ASM1369742v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:02:36,681] [INFO] Task succeeded: fastANI
[2023-06-18 11:02:36,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65689e9e-733b-4137-973e-1474eff755b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:02:36,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65689e9e-733b-4137-973e-1474eff755b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:02:36,685] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:02:36,686] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:02:36,686] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.7303	98	338	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:02:36,688] [INFO] DFAST Taxonomy check result was written to GCA_013697425.1_ASM1369742v1_genomic.fna/tc_result.tsv
[2023-06-18 11:02:36,689] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:02:36,689] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:02:36,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65689e9e-733b-4137-973e-1474eff755b5/dqc_reference/checkm_data
[2023-06-18 11:02:36,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:02:36,712] [INFO] Task started: CheckM
[2023-06-18 11:02:36,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013697425.1_ASM1369742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013697425.1_ASM1369742v1_genomic.fna/checkm_input GCA_013697425.1_ASM1369742v1_genomic.fna/checkm_result
[2023-06-18 11:02:56,829] [INFO] Task succeeded: CheckM
[2023-06-18 11:02:56,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:02:56,854] [INFO] ===== Completeness check finished =====
[2023-06-18 11:02:56,854] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:02:56,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013697425.1_ASM1369742v1_genomic.fna/markers.fasta)
[2023-06-18 11:02:56,855] [INFO] Task started: Blastn
[2023-06-18 11:02:56,855] [INFO] Running command: blastn -query GCA_013697425.1_ASM1369742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65689e9e-733b-4137-973e-1474eff755b5/dqc_reference/reference_markers_gtdb.fasta -out GCA_013697425.1_ASM1369742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:02:57,792] [INFO] Task succeeded: Blastn
[2023-06-18 11:02:57,796] [INFO] Selected 14 target genomes.
[2023-06-18 11:02:57,797] [INFO] Target genome list was writen to GCA_013697425.1_ASM1369742v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:02:57,836] [INFO] Task started: fastANI
[2023-06-18 11:02:57,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd4045d-3756-474e-a105-f0b811d82d4f/GCA_013697425.1_ASM1369742v1_genomic.fna.gz --refList GCA_013697425.1_ASM1369742v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013697425.1_ASM1369742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:03:04,758] [INFO] Task succeeded: fastANI
[2023-06-18 11:03:04,769] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 11:03:04,770] [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_017889745.1	s__JAGGAG01 sp017889745	77.5231	68	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JAGGAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013820855.1	s__JACDDX01 sp013820855	77.4517	90	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACDDX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816685.1	s__JACDDX01 sp013816685	77.4289	64	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACDDX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812695.1	s__JACDDX01 sp013812695	77.3691	98	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACDDX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011362545.1	s__DSTP01 sp011362545	77.2912	97	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__DSTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813145.1	s__JACDDX01 sp013813145	77.2466	57	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACDDX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713435.1	s__JADJOM01 sp016713435	77.1657	112	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JADJOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713785.1	s__JADJOM01 sp016713785	77.0821	105	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JADJOM01	95.0	99.05	98.46	0.95	0.91	10	-
GCA_016704275.1	s__Palsa-1233 sp016704275	77.0435	66	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__Palsa-1233	95.0	97.87	97.54	0.90	0.86	5	-
GCA_013694695.1	s__Palsa-1233 sp013694695	76.7839	57	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__Palsa-1233	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140635.1	s__JABFSM01 sp013140635	76.5007	64	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JABFSM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222035.1	s__AG41 sp003222035	76.0324	50	338	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	99.30	99.30	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-18 11:03:04,774] [INFO] GTDB search result was written to GCA_013697425.1_ASM1369742v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:03:04,775] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:03:04,779] [INFO] DFAST_QC result json was written to GCA_013697425.1_ASM1369742v1_genomic.fna/dqc_result.json
[2023-06-18 11:03:04,780] [INFO] DFAST_QC completed!
[2023-06-18 11:03:04,780] [INFO] Total running time: 0h0m46s