[2023-03-16 18:18:12,471] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:18:12,471] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:18:12,471] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4361aa9-fee2-406b-8a40-748170f57073/dqc_reference
[2023-03-16 18:18:13,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:18:13,605] [INFO] Task started: Prodigal
[2023-03-16 18:18:13,605] [INFO] Running command: cat /var/lib/cwl/stg9f9e6f7e-699e-4510-8362-c37c6d475119/OceanDNA-b18245.fa | prodigal -d OceanDNA-b18245/cds.fna -a OceanDNA-b18245/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:18:16,626] [INFO] Task succeeded: Prodigal
[2023-03-16 18:18:16,627] [INFO] Task started: HMMsearch
[2023-03-16 18:18:16,627] [INFO] Running command: hmmsearch --tblout OceanDNA-b18245/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4361aa9-fee2-406b-8a40-748170f57073/dqc_reference/reference_markers.hmm OceanDNA-b18245/protein.faa > /dev/null
[2023-03-16 18:18:16,759] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:18:16,759] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9f9e6f7e-699e-4510-8362-c37c6d475119/OceanDNA-b18245.fa]
[2023-03-16 18:18:16,765] [INFO] Query marker FASTA was written to OceanDNA-b18245/markers.fasta
[2023-03-16 18:18:16,768] [INFO] Task started: Blastn
[2023-03-16 18:18:16,768] [INFO] Running command: blastn -query OceanDNA-b18245/markers.fasta -db /var/lib/cwl/stgb4361aa9-fee2-406b-8a40-748170f57073/dqc_reference/reference_markers.fasta -out OceanDNA-b18245/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:18:17,299] [INFO] Task succeeded: Blastn
[2023-03-16 18:18:17,300] [INFO] Selected 17 target genomes.
[2023-03-16 18:18:17,301] [INFO] Target genome list was writen to OceanDNA-b18245/target_genomes.txt
[2023-03-16 18:18:17,317] [INFO] Task started: fastANI
[2023-03-16 18:18:17,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f9e6f7e-699e-4510-8362-c37c6d475119/OceanDNA-b18245.fa --refList OceanDNA-b18245/target_genomes.txt --output OceanDNA-b18245/fastani_result.tsv --threads 1
[2023-03-16 18:18:29,033] [INFO] Task succeeded: fastANI
[2023-03-16 18:18:29,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4361aa9-fee2-406b-8a40-748170f57073/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:18:29,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4361aa9-fee2-406b-8a40-748170f57073/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:18:29,034] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:18:29,034] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:18:29,034] [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
--------------------------------------------------------------------------------
[2023-03-16 18:18:29,035] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18245/tc_result.tsv
[2023-03-16 18:18:29,035] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:18:29,035] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:18:29,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4361aa9-fee2-406b-8a40-748170f57073/dqc_reference/checkm_data
[2023-03-16 18:18:29,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:18:29,040] [INFO] Task started: CheckM
[2023-03-16 18:18:29,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18245/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18245/checkm_input OceanDNA-b18245/checkm_result
[2023-03-16 18:18:54,203] [INFO] Task succeeded: CheckM
[2023-03-16 18:18:54,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:18:54,205] [INFO] ===== Completeness check finished =====
[2023-03-16 18:18:54,205] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:18:54,205] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18245/markers.fasta)
[2023-03-16 18:18:54,207] [INFO] Task started: Blastn
[2023-03-16 18:18:54,207] [INFO] Running command: blastn -query OceanDNA-b18245/markers.fasta -db /var/lib/cwl/stgb4361aa9-fee2-406b-8a40-748170f57073/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18245/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:18:55,087] [INFO] Task succeeded: Blastn
[2023-03-16 18:18:55,088] [INFO] Selected 6 target genomes.
[2023-03-16 18:18:55,088] [INFO] Target genome list was writen to OceanDNA-b18245/target_genomes_gtdb.txt
[2023-03-16 18:18:55,170] [INFO] Task started: fastANI
[2023-03-16 18:18:55,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f9e6f7e-699e-4510-8362-c37c6d475119/OceanDNA-b18245.fa --refList OceanDNA-b18245/target_genomes_gtdb.txt --output OceanDNA-b18245/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:18:56,252] [INFO] Task succeeded: fastANI
[2023-03-16 18:18:56,257] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:18:56,257] [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_000402655.1	s__Marinisoma sp000402655	98.6818	200	203	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	conclusive
GCA_902576865.1	s__Marinisoma sp902576865	88.5036	144	203	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.64	96.64	0.80	0.80	2	-
GCA_902599655.1	s__Marinisoma sp902599655	88.1173	130	203	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.53	97.28	0.66	0.66	3	-
GCA_902538565.1	s__Marinisoma sp902538565	88.0515	188	203	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.07	99.04	0.96	0.96	3	-
GCA_902525615.1	s__Marinisoma sp902525615	87.6955	165	203	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624275.1	s__Marinisoma sp902624275	86.2499	166	203	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:18:56,257] [INFO] GTDB search result was written to OceanDNA-b18245/result_gtdb.tsv
[2023-03-16 18:18:56,257] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:18:56,258] [INFO] DFAST_QC result json was written to OceanDNA-b18245/dqc_result.json
[2023-03-16 18:18:56,258] [INFO] DFAST_QC completed!
[2023-03-16 18:18:56,259] [INFO] Total running time: 0h0m44s