[2023-03-18 03:45:10,281] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,282] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,282] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8013df0-1eb4-4416-8fc6-7f2ceded99dc/dqc_reference
[2023-03-18 03:45:12,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,144] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,145] [INFO] Running command: cat /var/lib/cwl/stgf4558024-1792-48ef-a339-79f5e56d249c/OceanDNA-b6582.fa | prodigal -d OceanDNA-b6582/cds.fna -a OceanDNA-b6582/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:26,803] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:26,803] [INFO] Task started: HMMsearch
[2023-03-18 03:45:26,803] [INFO] Running command: hmmsearch --tblout OceanDNA-b6582/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8013df0-1eb4-4416-8fc6-7f2ceded99dc/dqc_reference/reference_markers.hmm OceanDNA-b6582/protein.faa > /dev/null
[2023-03-18 03:45:27,028] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:27,028] [INFO] Found 6/6 markers.
[2023-03-18 03:45:27,044] [INFO] Query marker FASTA was written to OceanDNA-b6582/markers.fasta
[2023-03-18 03:45:27,044] [INFO] Task started: Blastn
[2023-03-18 03:45:27,045] [INFO] Running command: blastn -query OceanDNA-b6582/markers.fasta -db /var/lib/cwl/stgd8013df0-1eb4-4416-8fc6-7f2ceded99dc/dqc_reference/reference_markers.fasta -out OceanDNA-b6582/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:27,602] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:27,603] [INFO] Selected 31 target genomes.
[2023-03-18 03:45:27,603] [INFO] Target genome list was writen to OceanDNA-b6582/target_genomes.txt
[2023-03-18 03:45:27,617] [INFO] Task started: fastANI
[2023-03-18 03:45:27,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4558024-1792-48ef-a339-79f5e56d249c/OceanDNA-b6582.fa --refList OceanDNA-b6582/target_genomes.txt --output OceanDNA-b6582/fastani_result.tsv --threads 1
[2023-03-18 03:45:45,130] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:45,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8013df0-1eb4-4416-8fc6-7f2ceded99dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:45,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8013df0-1eb4-4416-8fc6-7f2ceded99dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:45,134] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:45,134] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:45,134] [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
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.501	108	575	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:45,134] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6582/tc_result.tsv
[2023-03-18 03:45:45,134] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:45,134] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:45,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8013df0-1eb4-4416-8fc6-7f2ceded99dc/dqc_reference/checkm_data
[2023-03-18 03:45:45,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:45,142] [INFO] Task started: CheckM
[2023-03-18 03:45:45,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6582/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6582/checkm_input OceanDNA-b6582/checkm_result
[2023-03-18 03:46:25,153] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:25,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.17%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:25,156] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:25,157] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:25,157] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6582/markers.fasta)
[2023-03-18 03:46:25,157] [INFO] Task started: Blastn
[2023-03-18 03:46:25,157] [INFO] Running command: blastn -query OceanDNA-b6582/markers.fasta -db /var/lib/cwl/stgd8013df0-1eb4-4416-8fc6-7f2ceded99dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6582/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:25,954] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:25,955] [INFO] Selected 29 target genomes.
[2023-03-18 03:46:25,955] [INFO] Target genome list was writen to OceanDNA-b6582/target_genomes_gtdb.txt
[2023-03-18 03:46:26,203] [INFO] Task started: fastANI
[2023-03-18 03:46:26,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4558024-1792-48ef-a339-79f5e56d249c/OceanDNA-b6582.fa --refList OceanDNA-b6582/target_genomes_gtdb.txt --output OceanDNA-b6582/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:41,074] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:41,078] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:46:41,078] [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_002707025.1	s__IN17 sp002707025	77.034	165	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	-
GCA_002694465.1	s__IN17 sp002694465	76.5501	114	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCA_013002065.1	s__SMXJ01 sp013002065	76.5085	58	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440705.1	s__IN17 sp002440705	76.1356	80	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.92	99.92	0.93	0.93	2	-
GCF_900102055.1	s__Ulvibacter litoralis	75.7471	50	575	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:41,079] [INFO] GTDB search result was written to OceanDNA-b6582/result_gtdb.tsv
[2023-03-18 03:46:41,079] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:41,079] [INFO] DFAST_QC result json was written to OceanDNA-b6582/dqc_result.json
[2023-03-18 03:46:41,080] [INFO] DFAST_QC completed!
[2023-03-18 03:46:41,080] [INFO] Total running time: 0h1m31s