[2023-03-16 06:31:19,223] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:31:19,225] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:31:19,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg830297c6-8924-4a27-a9c2-bee5af71d12e/dqc_reference
[2023-03-16 06:31:20,365] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:31:20,366] [INFO] Task started: Prodigal
[2023-03-16 06:31:20,366] [INFO] Running command: cat /var/lib/cwl/stg76ae16c8-7b9d-4eef-935c-2b2830248516/OceanDNA-b31510.fa | prodigal -d OceanDNA-b31510/cds.fna -a OceanDNA-b31510/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:31:42,521] [INFO] Task succeeded: Prodigal
[2023-03-16 06:31:42,522] [INFO] Task started: HMMsearch
[2023-03-16 06:31:42,522] [INFO] Running command: hmmsearch --tblout OceanDNA-b31510/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg830297c6-8924-4a27-a9c2-bee5af71d12e/dqc_reference/reference_markers.hmm OceanDNA-b31510/protein.faa > /dev/null
[2023-03-16 06:31:42,747] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:31:42,748] [INFO] Found 6/6 markers.
[2023-03-16 06:31:42,895] [INFO] Query marker FASTA was written to OceanDNA-b31510/markers.fasta
[2023-03-16 06:31:42,895] [INFO] Task started: Blastn
[2023-03-16 06:31:42,895] [INFO] Running command: blastn -query OceanDNA-b31510/markers.fasta -db /var/lib/cwl/stg830297c6-8924-4a27-a9c2-bee5af71d12e/dqc_reference/reference_markers.fasta -out OceanDNA-b31510/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:31:43,490] [INFO] Task succeeded: Blastn
[2023-03-16 06:31:43,531] [INFO] Selected 19 target genomes.
[2023-03-16 06:31:43,531] [INFO] Target genome list was writen to OceanDNA-b31510/target_genomes.txt
[2023-03-16 06:31:43,544] [INFO] Task started: fastANI
[2023-03-16 06:31:43,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg76ae16c8-7b9d-4eef-935c-2b2830248516/OceanDNA-b31510.fa --refList OceanDNA-b31510/target_genomes.txt --output OceanDNA-b31510/fastani_result.tsv --threads 1
[2023-03-16 06:31:54,013] [INFO] Task succeeded: fastANI
[2023-03-16 06:31:54,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg830297c6-8924-4a27-a9c2-bee5af71d12e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:31:54,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg830297c6-8924-4a27-a9c2-bee5af71d12e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:31:54,017] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:31:54,017] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:31:54,017] [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
Pseudemcibacter aquimaris	strain=Y4	GCA_020748165.1	2857064	2857064	type	True	77.4785	208	1256	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:31:54,028] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31510/tc_result.tsv
[2023-03-16 06:31:54,042] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:31:54,042] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:31:54,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg830297c6-8924-4a27-a9c2-bee5af71d12e/dqc_reference/checkm_data
[2023-03-16 06:31:54,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:31:54,050] [INFO] Task started: CheckM
[2023-03-16 06:31:54,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31510/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31510/checkm_input OceanDNA-b31510/checkm_result
[2023-03-16 06:32:50,168] [INFO] Task succeeded: CheckM
[2023-03-16 06:32:50,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:32:50,218] [INFO] ===== Completeness check finished =====
[2023-03-16 06:32:50,218] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:32:50,219] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31510/markers.fasta)
[2023-03-16 06:32:50,219] [INFO] Task started: Blastn
[2023-03-16 06:32:50,219] [INFO] Running command: blastn -query OceanDNA-b31510/markers.fasta -db /var/lib/cwl/stg830297c6-8924-4a27-a9c2-bee5af71d12e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31510/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:32:51,185] [INFO] Task succeeded: Blastn
[2023-03-16 06:32:51,192] [INFO] Selected 19 target genomes.
[2023-03-16 06:32:51,192] [INFO] Target genome list was writen to OceanDNA-b31510/target_genomes_gtdb.txt
[2023-03-16 06:32:51,213] [INFO] Task started: fastANI
[2023-03-16 06:32:51,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg76ae16c8-7b9d-4eef-935c-2b2830248516/OceanDNA-b31510.fa --refList OceanDNA-b31510/target_genomes_gtdb.txt --output OceanDNA-b31510/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:32:58,716] [INFO] Task succeeded: fastANI
[2023-03-16 06:32:58,721] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:32:58,721] [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_018660225.1	s__UBA4441 sp018660225	77.8778	326	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.68	99.64	0.89	0.88	3	-
GCA_018675425.1	s__UBA4441 sp018675425	77.727	242	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.54	99.14	0.91	0.86	6	-
GCA_016763335.1	s__UBA4441 sp016763335	77.7016	290	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390425.1	s__UBA4441 sp002390425	77.6781	173	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.08	99.08	0.89	0.89	2	-
GCA_905612225.1	s__UBA4441 sp905612225	77.6011	123	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699075.1	s__UBA4441 sp018699075	77.1542	207	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.25	99.25	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-03-16 06:32:58,724] [INFO] GTDB search result was written to OceanDNA-b31510/result_gtdb.tsv
[2023-03-16 06:32:58,726] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:32:58,730] [INFO] DFAST_QC result json was written to OceanDNA-b31510/dqc_result.json
[2023-03-16 06:32:58,730] [INFO] DFAST_QC completed!
[2023-03-16 06:32:58,730] [INFO] Total running time: 0h1m40s