[2023-03-18 22:44:58,069] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:58,069] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:58,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg33a3597e-e6c0-414d-a20f-22ad72221df0/dqc_reference
[2023-03-18 22:44:59,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:59,190] [INFO] Task started: Prodigal
[2023-03-18 22:44:59,190] [INFO] Running command: cat /var/lib/cwl/stg494ecc10-a197-40fb-9ed2-0fa8adf88eff/OceanDNA-b2177.fa | prodigal -d OceanDNA-b2177/cds.fna -a OceanDNA-b2177/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:02,124] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:02,124] [INFO] Task started: HMMsearch
[2023-03-18 22:45:02,124] [INFO] Running command: hmmsearch --tblout OceanDNA-b2177/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33a3597e-e6c0-414d-a20f-22ad72221df0/dqc_reference/reference_markers.hmm OceanDNA-b2177/protein.faa > /dev/null
[2023-03-18 22:45:02,246] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:02,246] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg494ecc10-a197-40fb-9ed2-0fa8adf88eff/OceanDNA-b2177.fa]
[2023-03-18 22:45:02,263] [INFO] Query marker FASTA was written to OceanDNA-b2177/markers.fasta
[2023-03-18 22:45:02,264] [INFO] Task started: Blastn
[2023-03-18 22:45:02,264] [INFO] Running command: blastn -query OceanDNA-b2177/markers.fasta -db /var/lib/cwl/stg33a3597e-e6c0-414d-a20f-22ad72221df0/dqc_reference/reference_markers.fasta -out OceanDNA-b2177/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:02,696] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:02,699] [INFO] Selected 12 target genomes.
[2023-03-18 22:45:02,700] [INFO] Target genome list was writen to OceanDNA-b2177/target_genomes.txt
[2023-03-18 22:45:02,706] [INFO] Task started: fastANI
[2023-03-18 22:45:02,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg494ecc10-a197-40fb-9ed2-0fa8adf88eff/OceanDNA-b2177.fa --refList OceanDNA-b2177/target_genomes.txt --output OceanDNA-b2177/fastani_result.tsv --threads 1
[2023-03-18 22:45:06,733] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:06,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33a3597e-e6c0-414d-a20f-22ad72221df0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:06,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33a3597e-e6c0-414d-a20f-22ad72221df0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:06,734] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:06,734] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:45:06,734] [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
--------------------------------------------------------------------------------
[2023-03-18 22:45:06,736] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2177/tc_result.tsv
[2023-03-18 22:45:06,742] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:06,743] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:06,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33a3597e-e6c0-414d-a20f-22ad72221df0/dqc_reference/checkm_data
[2023-03-18 22:45:06,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:06,773] [INFO] Task started: CheckM
[2023-03-18 22:45:06,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2177/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2177/checkm_input OceanDNA-b2177/checkm_result
[2023-03-18 22:45:20,892] [INFO] Task succeeded: CheckM
[2023-03-18 22:45:20,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:45:20,894] [INFO] ===== Completeness check finished =====
[2023-03-18 22:45:20,895] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:45:20,895] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2177/markers.fasta)
[2023-03-18 22:45:20,895] [INFO] Task started: Blastn
[2023-03-18 22:45:20,895] [INFO] Running command: blastn -query OceanDNA-b2177/markers.fasta -db /var/lib/cwl/stg33a3597e-e6c0-414d-a20f-22ad72221df0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2177/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:21,346] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:21,351] [INFO] Selected 9 target genomes.
[2023-03-18 22:45:21,351] [INFO] Target genome list was writen to OceanDNA-b2177/target_genomes_gtdb.txt
[2023-03-18 22:45:21,363] [INFO] Task started: fastANI
[2023-03-18 22:45:21,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg494ecc10-a197-40fb-9ed2-0fa8adf88eff/OceanDNA-b2177.fa --refList OceanDNA-b2177/target_genomes_gtdb.txt --output OceanDNA-b2177/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:45:22,943] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:22,949] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:45:22,949] [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_004213405.1	s__Actinomarina sp004213405	99.1307	131	189	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902580215.1	s__Actinomarina sp902580215	93.5102	156	189	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.48	95.05	0.79	0.77	5	-
GCA_902593475.1	s__Actinomarina sp902593475	93.2207	136	189	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599555.1	s__Actinomarina sp902599555	92.8076	160	189	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777845.1	s__Actinomarina sp016777845	92.6143	124	189	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902610815.1	s__Actinomarina sp902610815	90.2046	166	189	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576605.1	s__Actinomarina sp902576605	89.2765	118	189	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628045.1	s__Actinomarina sp902628045	86.8646	148	189	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622665.1	s__Actinomarina sp902622665	86.6898	144	189	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:45:22,956] [INFO] GTDB search result was written to OceanDNA-b2177/result_gtdb.tsv
[2023-03-18 22:45:22,967] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:45:22,973] [INFO] DFAST_QC result json was written to OceanDNA-b2177/dqc_result.json
[2023-03-18 22:45:22,973] [INFO] DFAST_QC completed!
[2023-03-18 22:45:22,973] [INFO] Total running time: 0h0m25s