[2023-03-19 01:13:43,299] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:43,299] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:43,299] [INFO] DQC Reference Directory: /var/lib/cwl/stgeae29f64-1600-4b85-ae46-429c9b26d40b/dqc_reference
[2023-03-19 01:13:44,432] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:44,433] [INFO] Task started: Prodigal
[2023-03-19 01:13:44,433] [INFO] Running command: cat /var/lib/cwl/stg4e55c714-7a0a-4e0b-8d78-cef45f9d1832/OceanDNA-b21131.fa | prodigal -d OceanDNA-b21131/cds.fna -a OceanDNA-b21131/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:14:04,154] [INFO] Task succeeded: Prodigal
[2023-03-19 01:14:04,154] [INFO] Task started: HMMsearch
[2023-03-19 01:14:04,154] [INFO] Running command: hmmsearch --tblout OceanDNA-b21131/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeae29f64-1600-4b85-ae46-429c9b26d40b/dqc_reference/reference_markers.hmm OceanDNA-b21131/protein.faa > /dev/null
[2023-03-19 01:14:04,377] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:14:04,378] [INFO] Found 6/6 markers.
[2023-03-19 01:14:04,400] [INFO] Query marker FASTA was written to OceanDNA-b21131/markers.fasta
[2023-03-19 01:14:04,401] [INFO] Task started: Blastn
[2023-03-19 01:14:04,402] [INFO] Running command: blastn -query OceanDNA-b21131/markers.fasta -db /var/lib/cwl/stgeae29f64-1600-4b85-ae46-429c9b26d40b/dqc_reference/reference_markers.fasta -out OceanDNA-b21131/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:04,971] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:04,972] [INFO] Selected 19 target genomes.
[2023-03-19 01:14:04,972] [INFO] Target genome list was writen to OceanDNA-b21131/target_genomes.txt
[2023-03-19 01:14:04,990] [INFO] Task started: fastANI
[2023-03-19 01:14:04,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e55c714-7a0a-4e0b-8d78-cef45f9d1832/OceanDNA-b21131.fa --refList OceanDNA-b21131/target_genomes.txt --output OceanDNA-b21131/fastani_result.tsv --threads 1
[2023-03-19 01:14:15,836] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:15,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeae29f64-1600-4b85-ae46-429c9b26d40b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:14:15,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeae29f64-1600-4b85-ae46-429c9b26d40b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:14:15,837] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:14:15,837] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:14:15,837] [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
--------------------------------------------------------------------------------
[2023-03-19 01:14:15,838] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21131/tc_result.tsv
[2023-03-19 01:14:15,838] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:14:15,838] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:14:15,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeae29f64-1600-4b85-ae46-429c9b26d40b/dqc_reference/checkm_data
[2023-03-19 01:14:15,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:14:15,846] [INFO] Task started: CheckM
[2023-03-19 01:14:15,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21131/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21131/checkm_input OceanDNA-b21131/checkm_result
[2023-03-19 01:15:05,969] [INFO] Task succeeded: CheckM
[2023-03-19 01:15:05,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:15:05,973] [INFO] ===== Completeness check finished =====
[2023-03-19 01:15:05,973] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:15:05,973] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21131/markers.fasta)
[2023-03-19 01:15:05,974] [INFO] Task started: Blastn
[2023-03-19 01:15:05,974] [INFO] Running command: blastn -query OceanDNA-b21131/markers.fasta -db /var/lib/cwl/stgeae29f64-1600-4b85-ae46-429c9b26d40b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21131/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:15:07,033] [INFO] Task succeeded: Blastn
[2023-03-19 01:15:07,035] [INFO] Selected 10 target genomes.
[2023-03-19 01:15:07,035] [INFO] Target genome list was writen to OceanDNA-b21131/target_genomes_gtdb.txt
[2023-03-19 01:15:07,048] [INFO] Task started: fastANI
[2023-03-19 01:15:07,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e55c714-7a0a-4e0b-8d78-cef45f9d1832/OceanDNA-b21131.fa --refList OceanDNA-b21131/target_genomes_gtdb.txt --output OceanDNA-b21131/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:15:12,042] [INFO] Task succeeded: fastANI
[2023-03-19 01:15:12,048] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:15:12,048] [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_018673915.1	s__LS-NOB sp018673915	99.8727	963	1125	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.92	99.88	0.94	0.90	12	conclusive
GCA_018664975.1	s__LS-NOB sp018664975	86.7998	657	1125	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018653085.1	s__LS-NOB sp018653085	81.063	698	1125	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_003545625.1	s__LS-NOB sp003545625	80.4411	384	1125	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	98.65	98.65	0.77	0.77	2	-
GCA_001542995.1	s__LS-NOB sp001542995	79.4874	533	1125	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382285.1	s__LS-NOB sp014382285	79.2202	478	1125	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_012961055.1	s__LS-NOB sp012961055	78.4068	238	1125	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612265.1	s__LS-NOB sp905612265	77.9678	132	1125	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018702695.1	s__LS-NOB sp018702695	77.3114	296	1125	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.34	99.32	0.82	0.80	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:15:12,049] [INFO] GTDB search result was written to OceanDNA-b21131/result_gtdb.tsv
[2023-03-19 01:15:12,050] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:15:12,052] [INFO] DFAST_QC result json was written to OceanDNA-b21131/dqc_result.json
[2023-03-19 01:15:12,052] [INFO] DFAST_QC completed!
[2023-03-19 01:15:12,052] [INFO] Total running time: 0h1m29s