[2023-03-18 05:05:08,012] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:05:08,012] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:05:08,012] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb4bcdd6-b4bc-4211-8ed6-9653f7ebc9aa/dqc_reference
[2023-03-18 05:05:09,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:05:09,144] [INFO] Task started: Prodigal
[2023-03-18 05:05:09,144] [INFO] Running command: cat /var/lib/cwl/stg99956117-12e1-4b37-8288-ad5bcb85d000/OceanDNA-b401.fa | prodigal -d OceanDNA-b401/cds.fna -a OceanDNA-b401/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:05:15,324] [INFO] Task succeeded: Prodigal
[2023-03-18 05:05:15,325] [INFO] Task started: HMMsearch
[2023-03-18 05:05:15,325] [INFO] Running command: hmmsearch --tblout OceanDNA-b401/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb4bcdd6-b4bc-4211-8ed6-9653f7ebc9aa/dqc_reference/reference_markers.hmm OceanDNA-b401/protein.faa > /dev/null
[2023-03-18 05:05:15,475] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:05:15,476] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg99956117-12e1-4b37-8288-ad5bcb85d000/OceanDNA-b401.fa]
[2023-03-18 05:05:15,492] [INFO] Query marker FASTA was written to OceanDNA-b401/markers.fasta
[2023-03-18 05:05:15,492] [INFO] Task started: Blastn
[2023-03-18 05:05:15,492] [INFO] Running command: blastn -query OceanDNA-b401/markers.fasta -db /var/lib/cwl/stgfb4bcdd6-b4bc-4211-8ed6-9653f7ebc9aa/dqc_reference/reference_markers.fasta -out OceanDNA-b401/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:15,989] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:15,992] [INFO] Selected 19 target genomes.
[2023-03-18 05:05:15,992] [INFO] Target genome list was writen to OceanDNA-b401/target_genomes.txt
[2023-03-18 05:05:16,026] [INFO] Task started: fastANI
[2023-03-18 05:05:16,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg99956117-12e1-4b37-8288-ad5bcb85d000/OceanDNA-b401.fa --refList OceanDNA-b401/target_genomes.txt --output OceanDNA-b401/fastani_result.tsv --threads 1
[2023-03-18 05:05:31,272] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:31,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb4bcdd6-b4bc-4211-8ed6-9653f7ebc9aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:05:31,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb4bcdd6-b4bc-4211-8ed6-9653f7ebc9aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:05:31,273] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:05:31,273] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:05:31,273] [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 05:05:31,274] [INFO] DFAST Taxonomy check result was written to OceanDNA-b401/tc_result.tsv
[2023-03-18 05:05:31,276] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:05:31,276] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:05:31,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb4bcdd6-b4bc-4211-8ed6-9653f7ebc9aa/dqc_reference/checkm_data
[2023-03-18 05:05:31,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:05:31,330] [INFO] Task started: CheckM
[2023-03-18 05:05:31,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b401/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b401/checkm_input OceanDNA-b401/checkm_result
[2023-03-18 05:05:53,199] [INFO] Task succeeded: CheckM
[2023-03-18 05:05:53,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.08%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 05:05:53,238] [INFO] ===== Completeness check finished =====
[2023-03-18 05:05:53,238] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:05:53,238] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b401/markers.fasta)
[2023-03-18 05:05:53,239] [INFO] Task started: Blastn
[2023-03-18 05:05:53,239] [INFO] Running command: blastn -query OceanDNA-b401/markers.fasta -db /var/lib/cwl/stgfb4bcdd6-b4bc-4211-8ed6-9653f7ebc9aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b401/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:53,884] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:53,888] [INFO] Selected 12 target genomes.
[2023-03-18 05:05:53,888] [INFO] Target genome list was writen to OceanDNA-b401/target_genomes_gtdb.txt
[2023-03-18 05:05:54,052] [INFO] Task started: fastANI
[2023-03-18 05:05:54,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg99956117-12e1-4b37-8288-ad5bcb85d000/OceanDNA-b401.fa --refList OceanDNA-b401/target_genomes_gtdb.txt --output OceanDNA-b401/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:05:59,125] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:59,129] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:05:59,129] [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_012269985.1	s__Casp-actino5 sp012269985	92.4414	191	204	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.07	98.07	0.92	0.92	2	-
GCA_002727235.1	s__Casp-actino5 sp002727235	92.2175	175	204	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	97.22	95.99	0.84	0.77	5	-
GCA_002501485.1	s__Casp-actino5 sp002501485	90.2674	190	204	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.77	99.74	0.92	0.90	3	-
GCA_001510385.1	s__Casp-actino5 sp001510385	79.3109	94	204	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.68	99.68	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 05:05:59,131] [INFO] GTDB search result was written to OceanDNA-b401/result_gtdb.tsv
[2023-03-18 05:05:59,132] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:05:59,135] [INFO] DFAST_QC result json was written to OceanDNA-b401/dqc_result.json
[2023-03-18 05:05:59,135] [INFO] DFAST_QC completed!
[2023-03-18 05:05:59,135] [INFO] Total running time: 0h0m51s