[2023-03-16 02:38:04,891] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,891] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,891] [INFO] DQC Reference Directory: /var/lib/cwl/stgd71dc41b-5206-4929-bca3-814efc1ecc17/dqc_reference
[2023-03-16 02:38:05,984] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:05,984] [INFO] Task started: Prodigal
[2023-03-16 02:38:05,984] [INFO] Running command: cat /var/lib/cwl/stgee3d9603-5fbb-405b-837e-dcd33b35762a/OceanDNA-b45992.fa | prodigal -d OceanDNA-b45992/cds.fna -a OceanDNA-b45992/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:20,285] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:20,285] [INFO] Task started: HMMsearch
[2023-03-16 02:38:20,285] [INFO] Running command: hmmsearch --tblout OceanDNA-b45992/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd71dc41b-5206-4929-bca3-814efc1ecc17/dqc_reference/reference_markers.hmm OceanDNA-b45992/protein.faa > /dev/null
[2023-03-16 02:38:20,452] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:20,453] [INFO] Found 6/6 markers.
[2023-03-16 02:38:20,465] [INFO] Query marker FASTA was written to OceanDNA-b45992/markers.fasta
[2023-03-16 02:38:20,466] [INFO] Task started: Blastn
[2023-03-16 02:38:20,466] [INFO] Running command: blastn -query OceanDNA-b45992/markers.fasta -db /var/lib/cwl/stgd71dc41b-5206-4929-bca3-814efc1ecc17/dqc_reference/reference_markers.fasta -out OceanDNA-b45992/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:21,044] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:21,045] [INFO] Selected 24 target genomes.
[2023-03-16 02:38:21,045] [INFO] Target genome list was writen to OceanDNA-b45992/target_genomes.txt
[2023-03-16 02:38:21,056] [INFO] Task started: fastANI
[2023-03-16 02:38:21,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgee3d9603-5fbb-405b-837e-dcd33b35762a/OceanDNA-b45992.fa --refList OceanDNA-b45992/target_genomes.txt --output OceanDNA-b45992/fastani_result.tsv --threads 1
[2023-03-16 02:38:36,701] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:36,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd71dc41b-5206-4929-bca3-814efc1ecc17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:36,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd71dc41b-5206-4929-bca3-814efc1ecc17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:36,704] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:36,704] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 02:38:36,704] [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	76.3561	71	550	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:36,704] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45992/tc_result.tsv
[2023-03-16 02:38:36,704] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:36,704] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:36,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd71dc41b-5206-4929-bca3-814efc1ecc17/dqc_reference/checkm_data
[2023-03-16 02:38:36,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:36,708] [INFO] Task started: CheckM
[2023-03-16 02:38:36,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45992/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45992/checkm_input OceanDNA-b45992/checkm_result
[2023-03-16 02:39:16,820] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:16,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:16,822] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:16,822] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:16,822] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45992/markers.fasta)
[2023-03-16 02:39:16,822] [INFO] Task started: Blastn
[2023-03-16 02:39:16,822] [INFO] Running command: blastn -query OceanDNA-b45992/markers.fasta -db /var/lib/cwl/stgd71dc41b-5206-4929-bca3-814efc1ecc17/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45992/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:17,804] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:17,805] [INFO] Selected 8 target genomes.
[2023-03-16 02:39:17,805] [INFO] Target genome list was writen to OceanDNA-b45992/target_genomes_gtdb.txt
[2023-03-16 02:39:18,004] [INFO] Task started: fastANI
[2023-03-16 02:39:18,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgee3d9603-5fbb-405b-837e-dcd33b35762a/OceanDNA-b45992.fa --refList OceanDNA-b45992/target_genomes_gtdb.txt --output OceanDNA-b45992/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:22,511] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:22,516] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:39:22,517] [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_905182435.1	s__BACL24 sp905182435	98.8219	406	550	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017854655.1	s__BACL24 sp017854655	91.1898	464	550	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.39	99.26	0.93	0.92	3	-
GCA_018663485.1	s__BACL24 sp018663485	90.8289	420	550	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430605.1	s__BACL24 sp002430605	89.6689	481	550	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.69	99.69	0.90	0.90	2	-
GCA_002292345.1	s__BACL24 sp002292345	88.5623	440	550	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.51	99.36	0.91	0.87	10	-
GCA_905479975.1	s__BACL24 sp905479975	80.7756	360	550	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902728235.1	s__BACL24 sp902728235	80.1725	332	550	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.30	98.39	0.95	0.90	8	-
GCA_002729725.1	s__UBA7441 sp002729725	77.3029	114	550	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	99.86	99.86	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-16 02:39:22,517] [INFO] GTDB search result was written to OceanDNA-b45992/result_gtdb.tsv
[2023-03-16 02:39:22,517] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:22,518] [INFO] DFAST_QC result json was written to OceanDNA-b45992/dqc_result.json
[2023-03-16 02:39:22,518] [INFO] DFAST_QC completed!
[2023-03-16 02:39:22,518] [INFO] Total running time: 0h1m18s