[2023-03-18 23:56:04,497] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:56:04,497] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:56:04,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1c77170-00bc-4511-919a-0a5a1333ca28/dqc_reference
[2023-03-18 23:56:05,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:56:05,621] [INFO] Task started: Prodigal
[2023-03-18 23:56:05,621] [INFO] Running command: cat /var/lib/cwl/stgf8be007b-424b-4fed-a798-69b18b58c2bf/OceanDNA-b15447.fa | prodigal -d OceanDNA-b15447/cds.fna -a OceanDNA-b15447/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:56:14,067] [INFO] Task succeeded: Prodigal
[2023-03-18 23:56:14,067] [INFO] Task started: HMMsearch
[2023-03-18 23:56:14,067] [INFO] Running command: hmmsearch --tblout OceanDNA-b15447/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1c77170-00bc-4511-919a-0a5a1333ca28/dqc_reference/reference_markers.hmm OceanDNA-b15447/protein.faa > /dev/null
[2023-03-18 23:56:14,221] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:56:14,222] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf8be007b-424b-4fed-a798-69b18b58c2bf/OceanDNA-b15447.fa]
[2023-03-18 23:56:14,233] [INFO] Query marker FASTA was written to OceanDNA-b15447/markers.fasta
[2023-03-18 23:56:14,235] [INFO] Task started: Blastn
[2023-03-18 23:56:14,235] [INFO] Running command: blastn -query OceanDNA-b15447/markers.fasta -db /var/lib/cwl/stgd1c77170-00bc-4511-919a-0a5a1333ca28/dqc_reference/reference_markers.fasta -out OceanDNA-b15447/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:56:14,718] [INFO] Task succeeded: Blastn
[2023-03-18 23:56:14,719] [INFO] Selected 5 target genomes.
[2023-03-18 23:56:14,719] [INFO] Target genome list was writen to OceanDNA-b15447/target_genomes.txt
[2023-03-18 23:56:14,722] [INFO] Task started: fastANI
[2023-03-18 23:56:14,722] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8be007b-424b-4fed-a798-69b18b58c2bf/OceanDNA-b15447.fa --refList OceanDNA-b15447/target_genomes.txt --output OceanDNA-b15447/fastani_result.tsv --threads 1
[2023-03-18 23:56:17,688] [INFO] Task succeeded: fastANI
[2023-03-18 23:56:17,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1c77170-00bc-4511-919a-0a5a1333ca28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:56:17,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1c77170-00bc-4511-919a-0a5a1333ca28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:56:17,689] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:56:17,689] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:56:17,689] [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 23:56:17,690] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15447/tc_result.tsv
[2023-03-18 23:56:17,690] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:56:17,690] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:56:17,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1c77170-00bc-4511-919a-0a5a1333ca28/dqc_reference/checkm_data
[2023-03-18 23:56:17,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:56:17,696] [INFO] Task started: CheckM
[2023-03-18 23:56:17,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15447/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15447/checkm_input OceanDNA-b15447/checkm_result
[2023-03-18 23:56:43,349] [INFO] Task succeeded: CheckM
[2023-03-18 23:56:43,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:56:43,351] [INFO] ===== Completeness check finished =====
[2023-03-18 23:56:43,351] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:56:43,351] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15447/markers.fasta)
[2023-03-18 23:56:43,352] [INFO] Task started: Blastn
[2023-03-18 23:56:43,353] [INFO] Running command: blastn -query OceanDNA-b15447/markers.fasta -db /var/lib/cwl/stgd1c77170-00bc-4511-919a-0a5a1333ca28/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15447/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:56:43,955] [INFO] Task succeeded: Blastn
[2023-03-18 23:56:43,956] [INFO] Selected 17 target genomes.
[2023-03-18 23:56:43,956] [INFO] Target genome list was writen to OceanDNA-b15447/target_genomes_gtdb.txt
[2023-03-18 23:56:43,971] [INFO] Task started: fastANI
[2023-03-18 23:56:43,972] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8be007b-424b-4fed-a798-69b18b58c2bf/OceanDNA-b15447.fa --refList OceanDNA-b15447/target_genomes_gtdb.txt --output OceanDNA-b15447/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:56:48,262] [INFO] Task succeeded: fastANI
[2023-03-18 23:56:48,264] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:56:48,265] [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_003523055.1	s__UBA2588 sp003523055	99.845	518	524	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA2588;g__UBA2588	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002339805.1	s__UBA2588 sp002339805	77.5808	66	524	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA2588;g__UBA2588	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:56:48,431] [INFO] GTDB search result was written to OceanDNA-b15447/result_gtdb.tsv
[2023-03-18 23:56:48,682] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:56:48,682] [INFO] DFAST_QC result json was written to OceanDNA-b15447/dqc_result.json
[2023-03-18 23:56:48,683] [INFO] DFAST_QC completed!
[2023-03-18 23:56:48,683] [INFO] Total running time: 0h0m44s