[2023-03-18 22:26:05,785] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:26:05,785] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:26:05,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d4c3f64-0115-441c-b498-53653531879c/dqc_reference
[2023-03-18 22:26:06,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:26:06,944] [INFO] Task started: Prodigal
[2023-03-18 22:26:06,945] [INFO] Running command: cat /var/lib/cwl/stgb001ffec-1d27-47cc-8e20-d4af94af44d8/OceanDNA-b41707.fa | prodigal -d OceanDNA-b41707/cds.fna -a OceanDNA-b41707/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:26:11,432] [INFO] Task succeeded: Prodigal
[2023-03-18 22:26:11,432] [INFO] Task started: HMMsearch
[2023-03-18 22:26:11,432] [INFO] Running command: hmmsearch --tblout OceanDNA-b41707/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d4c3f64-0115-441c-b498-53653531879c/dqc_reference/reference_markers.hmm OceanDNA-b41707/protein.faa > /dev/null
[2023-03-18 22:26:11,671] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:26:11,672] [INFO] Found 6/6 markers.
[2023-03-18 22:26:11,692] [INFO] Query marker FASTA was written to OceanDNA-b41707/markers.fasta
[2023-03-18 22:26:11,721] [INFO] Task started: Blastn
[2023-03-18 22:26:11,721] [INFO] Running command: blastn -query OceanDNA-b41707/markers.fasta -db /var/lib/cwl/stg9d4c3f64-0115-441c-b498-53653531879c/dqc_reference/reference_markers.fasta -out OceanDNA-b41707/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:26:12,315] [INFO] Task succeeded: Blastn
[2023-03-18 22:26:12,318] [INFO] Selected 22 target genomes.
[2023-03-18 22:26:12,318] [INFO] Target genome list was writen to OceanDNA-b41707/target_genomes.txt
[2023-03-18 22:26:12,338] [INFO] Task started: fastANI
[2023-03-18 22:26:12,338] [INFO] Running command: fastANI --query /var/lib/cwl/stgb001ffec-1d27-47cc-8e20-d4af94af44d8/OceanDNA-b41707.fa --refList OceanDNA-b41707/target_genomes.txt --output OceanDNA-b41707/fastani_result.tsv --threads 1
[2023-03-18 22:26:20,977] [INFO] Task succeeded: fastANI
[2023-03-18 22:26:20,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d4c3f64-0115-441c-b498-53653531879c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:26:20,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d4c3f64-0115-441c-b498-53653531879c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:26:20,978] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:26:20,978] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:26:20,978] [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 22:26:20,979] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41707/tc_result.tsv
[2023-03-18 22:26:20,981] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:26:20,981] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:26:20,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d4c3f64-0115-441c-b498-53653531879c/dqc_reference/checkm_data
[2023-03-18 22:26:20,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:26:20,992] [INFO] Task started: CheckM
[2023-03-18 22:26:20,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41707/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41707/checkm_input OceanDNA-b41707/checkm_result
[2023-03-18 22:26:38,346] [INFO] Task succeeded: CheckM
[2023-03-18 22:26:38,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.01%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:26:38,429] [INFO] ===== Completeness check finished =====
[2023-03-18 22:26:38,429] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:26:38,430] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41707/markers.fasta)
[2023-03-18 22:26:38,431] [INFO] Task started: Blastn
[2023-03-18 22:26:38,431] [INFO] Running command: blastn -query OceanDNA-b41707/markers.fasta -db /var/lib/cwl/stg9d4c3f64-0115-441c-b498-53653531879c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41707/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:26:39,265] [INFO] Task succeeded: Blastn
[2023-03-18 22:26:39,269] [INFO] Selected 14 target genomes.
[2023-03-18 22:26:39,269] [INFO] Target genome list was writen to OceanDNA-b41707/target_genomes_gtdb.txt
[2023-03-18 22:26:39,287] [INFO] Task started: fastANI
[2023-03-18 22:26:39,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgb001ffec-1d27-47cc-8e20-d4af94af44d8/OceanDNA-b41707.fa --refList OceanDNA-b41707/target_genomes_gtdb.txt --output OceanDNA-b41707/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:26:42,444] [INFO] Task succeeded: fastANI
[2023-03-18 22:26:42,453] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:26:42,453] [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_003279605.1	s__MEDG-81 sp003279605	85.4133	264	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902561325.1	s__MEDG-81 sp902561325	85.3023	222	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	98.13	98.13	0.81	0.81	2	-
GCA_003213595.1	s__MEDG-81 sp003213595	84.8518	236	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	99.82	99.63	0.96	0.91	3	-
GCA_902587545.1	s__MEDG-81 sp902587545	84.7071	231	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625415.1	s__MEDG-81 sp902625415	84.523	238	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514765.1	s__MEDG-81 sp902514765	84.3145	172	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902540995.1	s__MEDG-81 sp902540995	84.2695	192	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	98.42	98.42	0.80	0.80	2	-
GCA_002689405.1	s__MEDG-81 sp002689405	84.1997	220	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902629465.1	s__MEDG-81 sp902629465	84.1461	180	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902632605.1	s__MEDG-81 sp902632605	84.1209	242	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595715.1	s__MEDG-81 sp902595715	84.0533	232	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514645.1	s__MEDG-81 sp902514645	83.9841	172	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627595.1	s__MEDG-81 sp902627595	83.4192	207	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	97.00	97.00	0.78	0.78	2	-
GCA_902563105.1	s__MEDG-81 sp902563105	80.3974	176	282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	96.75	96.64	0.93	0.92	5	-
--------------------------------------------------------------------------------
[2023-03-18 22:26:42,455] [INFO] GTDB search result was written to OceanDNA-b41707/result_gtdb.tsv
[2023-03-18 22:26:42,457] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:26:42,459] [INFO] DFAST_QC result json was written to OceanDNA-b41707/dqc_result.json
[2023-03-18 22:26:42,459] [INFO] DFAST_QC completed!
[2023-03-18 22:26:42,459] [INFO] Total running time: 0h0m37s