[2023-03-16 18:27:22,234] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:27:22,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:27:22,234] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb648855-3cc9-4f81-a34d-7302b2f1a139/dqc_reference
[2023-03-16 18:27:25,011] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:27:25,011] [INFO] Task started: Prodigal
[2023-03-16 18:27:25,012] [INFO] Running command: cat /var/lib/cwl/stga336a72e-abed-4bb9-a84c-51114ace484d/OceanDNA-b17440.fa | prodigal -d OceanDNA-b17440/cds.fna -a OceanDNA-b17440/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:27:34,275] [INFO] Task succeeded: Prodigal
[2023-03-16 18:27:34,276] [INFO] Task started: HMMsearch
[2023-03-16 18:27:34,276] [INFO] Running command: hmmsearch --tblout OceanDNA-b17440/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb648855-3cc9-4f81-a34d-7302b2f1a139/dqc_reference/reference_markers.hmm OceanDNA-b17440/protein.faa > /dev/null
[2023-03-16 18:27:34,473] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:27:34,473] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga336a72e-abed-4bb9-a84c-51114ace484d/OceanDNA-b17440.fa]
[2023-03-16 18:27:34,485] [INFO] Query marker FASTA was written to OceanDNA-b17440/markers.fasta
[2023-03-16 18:27:34,485] [INFO] Task started: Blastn
[2023-03-16 18:27:34,485] [INFO] Running command: blastn -query OceanDNA-b17440/markers.fasta -db /var/lib/cwl/stgcb648855-3cc9-4f81-a34d-7302b2f1a139/dqc_reference/reference_markers.fasta -out OceanDNA-b17440/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:27:35,015] [INFO] Task succeeded: Blastn
[2023-03-16 18:27:35,016] [INFO] Selected 7 target genomes.
[2023-03-16 18:27:35,016] [INFO] Target genome list was writen to OceanDNA-b17440/target_genomes.txt
[2023-03-16 18:27:35,020] [INFO] Task started: fastANI
[2023-03-16 18:27:35,020] [INFO] Running command: fastANI --query /var/lib/cwl/stga336a72e-abed-4bb9-a84c-51114ace484d/OceanDNA-b17440.fa --refList OceanDNA-b17440/target_genomes.txt --output OceanDNA-b17440/fastani_result.tsv --threads 1
[2023-03-16 18:27:38,660] [INFO] Task succeeded: fastANI
[2023-03-16 18:27:38,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb648855-3cc9-4f81-a34d-7302b2f1a139/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:27:38,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb648855-3cc9-4f81-a34d-7302b2f1a139/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:27:38,661] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:27:38,661] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:27:38,661] [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
--------------------------------------------------------------------------------
[2023-03-16 18:27:38,661] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17440/tc_result.tsv
[2023-03-16 18:27:38,661] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:27:38,661] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:27:38,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb648855-3cc9-4f81-a34d-7302b2f1a139/dqc_reference/checkm_data
[2023-03-16 18:27:38,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:27:38,668] [INFO] Task started: CheckM
[2023-03-16 18:27:38,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17440/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17440/checkm_input OceanDNA-b17440/checkm_result
[2023-03-16 18:28:07,397] [INFO] Task succeeded: CheckM
[2023-03-16 18:28:07,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.31%
Contamintation: 2.46%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 18:28:07,399] [INFO] ===== Completeness check finished =====
[2023-03-16 18:28:07,399] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:28:07,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17440/markers.fasta)
[2023-03-16 18:28:07,399] [INFO] Task started: Blastn
[2023-03-16 18:28:07,399] [INFO] Running command: blastn -query OceanDNA-b17440/markers.fasta -db /var/lib/cwl/stgcb648855-3cc9-4f81-a34d-7302b2f1a139/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17440/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:28:08,722] [INFO] Task succeeded: Blastn
[2023-03-16 18:28:08,723] [INFO] Selected 5 target genomes.
[2023-03-16 18:28:08,723] [INFO] Target genome list was writen to OceanDNA-b17440/target_genomes_gtdb.txt
[2023-03-16 18:28:08,730] [INFO] Task started: fastANI
[2023-03-16 18:28:08,730] [INFO] Running command: fastANI --query /var/lib/cwl/stga336a72e-abed-4bb9-a84c-51114ace484d/OceanDNA-b17440.fa --refList OceanDNA-b17440/target_genomes_gtdb.txt --output OceanDNA-b17440/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:28:11,488] [INFO] Task succeeded: fastANI
[2023-03-16 18:28:11,492] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:28:11,492] [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_002724575.1	s__UBA1138 sp002724575	93.4231	310	348	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	96.61	95.09	0.77	0.73	4	-
GCA_002313925.1	s__UBA1138 sp002313925	87.9851	320	348	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	96.15	95.66	0.87	0.85	5	-
GCA_012960225.1	s__UBA1138 sp012960225	87.634	333	348	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.89	99.89	0.95	0.95	2	-
GCA_002501085.1	s__UBA1138 sp002501085	87.4859	322	348	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	98.27	98.27	0.83	0.83	2	-
GCA_002311875.1	s__UBA1138 sp002311875	79.6581	267	348	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.17	99.17	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-16 18:28:11,492] [INFO] GTDB search result was written to OceanDNA-b17440/result_gtdb.tsv
[2023-03-16 18:28:11,492] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:28:11,493] [INFO] DFAST_QC result json was written to OceanDNA-b17440/dqc_result.json
[2023-03-16 18:28:11,493] [INFO] DFAST_QC completed!
[2023-03-16 18:28:11,493] [INFO] Total running time: 0h0m49s