[2023-03-15 20:34:26,716] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,716] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a311906-e317-4656-a57c-28b88e9c7ac1/dqc_reference
[2023-03-15 20:34:28,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,459] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,459] [INFO] Running command: cat /var/lib/cwl/stg08cb2832-052b-4c87-bd8a-ad93de667973/OceanDNA-b46177.fa | prodigal -d OceanDNA-b46177/cds.fna -a OceanDNA-b46177/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:43,346] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:43,346] [INFO] Task started: HMMsearch
[2023-03-15 20:34:43,346] [INFO] Running command: hmmsearch --tblout OceanDNA-b46177/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a311906-e317-4656-a57c-28b88e9c7ac1/dqc_reference/reference_markers.hmm OceanDNA-b46177/protein.faa > /dev/null
[2023-03-15 20:34:43,509] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:43,510] [INFO] Found 6/6 markers.
[2023-03-15 20:34:43,522] [INFO] Query marker FASTA was written to OceanDNA-b46177/markers.fasta
[2023-03-15 20:34:43,523] [INFO] Task started: Blastn
[2023-03-15 20:34:43,523] [INFO] Running command: blastn -query OceanDNA-b46177/markers.fasta -db /var/lib/cwl/stg4a311906-e317-4656-a57c-28b88e9c7ac1/dqc_reference/reference_markers.fasta -out OceanDNA-b46177/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:44,061] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:44,061] [INFO] Selected 19 target genomes.
[2023-03-15 20:34:44,061] [INFO] Target genome list was writen to OceanDNA-b46177/target_genomes.txt
[2023-03-15 20:34:44,073] [INFO] Task started: fastANI
[2023-03-15 20:34:44,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg08cb2832-052b-4c87-bd8a-ad93de667973/OceanDNA-b46177.fa --refList OceanDNA-b46177/target_genomes.txt --output OceanDNA-b46177/fastani_result.tsv --threads 1
[2023-03-15 20:34:56,304] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:56,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a311906-e317-4656-a57c-28b88e9c7ac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:56,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a311906-e317-4656-a57c-28b88e9c7ac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:56,308] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:56,308] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 20:34:56,308] [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
Coraliomargarita akajimensis	strain=DSM 45221	GCA_000025905.1	395922	395922	type	True	76.7072	54	574	95	below_threshold
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.5776	79	574	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:34:56,308] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46177/tc_result.tsv
[2023-03-15 20:34:56,309] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:56,309] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:56,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a311906-e317-4656-a57c-28b88e9c7ac1/dqc_reference/checkm_data
[2023-03-15 20:34:56,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:56,313] [INFO] Task started: CheckM
[2023-03-15 20:34:56,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46177/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46177/checkm_input OceanDNA-b46177/checkm_result
[2023-03-15 20:35:36,726] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:36,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:36,728] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:36,728] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:36,728] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46177/markers.fasta)
[2023-03-15 20:35:36,729] [INFO] Task started: Blastn
[2023-03-15 20:35:36,729] [INFO] Running command: blastn -query OceanDNA-b46177/markers.fasta -db /var/lib/cwl/stg4a311906-e317-4656-a57c-28b88e9c7ac1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46177/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:37,580] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:37,580] [INFO] Selected 19 target genomes.
[2023-03-15 20:35:37,581] [INFO] Target genome list was writen to OceanDNA-b46177/target_genomes_gtdb.txt
[2023-03-15 20:35:38,108] [INFO] Task started: fastANI
[2023-03-15 20:35:38,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg08cb2832-052b-4c87-bd8a-ad93de667973/OceanDNA-b46177.fa --refList OceanDNA-b46177/target_genomes_gtdb.txt --output OceanDNA-b46177/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:47,988] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:47,993] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:35:47,993] [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_002470925.1	s__UBA7445 sp002470925	91.2333	326	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7445	95.0	99.71	99.71	0.92	0.92	2	-
GCA_009937095.1	s__UBA7445 sp009937095	79.7861	301	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7445	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025905.1	s__Coraliomargarita akajimensis	76.7072	54	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__Coraliomargarita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908325.1	s__UBA7441 sp009908325	76.2582	64	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402305.1	s__UBA7441 sp018402305	76.2508	54	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003566795.1	s__WN38 sp003566795	76.241	55	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692545.1	s__UBA7441 sp007692545	76.0895	58	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:47,993] [INFO] GTDB search result was written to OceanDNA-b46177/result_gtdb.tsv
[2023-03-15 20:35:47,993] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:47,994] [INFO] DFAST_QC result json was written to OceanDNA-b46177/dqc_result.json
[2023-03-15 20:35:47,994] [INFO] DFAST_QC completed!
[2023-03-15 20:35:47,994] [INFO] Total running time: 0h1m21s