[2023-03-19 01:50:01,529] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,530] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg438fa397-5f1a-465c-8bf7-2be531a29d92/dqc_reference
[2023-03-19 01:50:02,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:02,653] [INFO] Task started: Prodigal
[2023-03-19 01:50:02,653] [INFO] Running command: cat /var/lib/cwl/stg94bbc994-e3fe-4185-a47e-9b31a1ad9e94/OceanDNA-b33770.fa | prodigal -d OceanDNA-b33770/cds.fna -a OceanDNA-b33770/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:06,119] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:06,119] [INFO] Task started: HMMsearch
[2023-03-19 01:50:06,119] [INFO] Running command: hmmsearch --tblout OceanDNA-b33770/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg438fa397-5f1a-465c-8bf7-2be531a29d92/dqc_reference/reference_markers.hmm OceanDNA-b33770/protein.faa > /dev/null
[2023-03-19 01:50:06,278] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:06,278] [INFO] Found 6/6 markers.
[2023-03-19 01:50:06,287] [INFO] Query marker FASTA was written to OceanDNA-b33770/markers.fasta
[2023-03-19 01:50:06,287] [INFO] Task started: Blastn
[2023-03-19 01:50:06,287] [INFO] Running command: blastn -query OceanDNA-b33770/markers.fasta -db /var/lib/cwl/stg438fa397-5f1a-465c-8bf7-2be531a29d92/dqc_reference/reference_markers.fasta -out OceanDNA-b33770/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:06,815] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:06,816] [INFO] Selected 30 target genomes.
[2023-03-19 01:50:06,816] [INFO] Target genome list was writen to OceanDNA-b33770/target_genomes.txt
[2023-03-19 01:50:06,836] [INFO] Task started: fastANI
[2023-03-19 01:50:06,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg94bbc994-e3fe-4185-a47e-9b31a1ad9e94/OceanDNA-b33770.fa --refList OceanDNA-b33770/target_genomes.txt --output OceanDNA-b33770/fastani_result.tsv --threads 1
[2023-03-19 01:50:21,265] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:21,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg438fa397-5f1a-465c-8bf7-2be531a29d92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:21,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg438fa397-5f1a-465c-8bf7-2be531a29d92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:21,266] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:21,266] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:50:21,266] [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
--------------------------------------------------------------------------------
[2023-03-19 01:50:21,266] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33770/tc_result.tsv
[2023-03-19 01:50:21,267] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:21,267] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:21,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg438fa397-5f1a-465c-8bf7-2be531a29d92/dqc_reference/checkm_data
[2023-03-19 01:50:21,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:21,272] [INFO] Task started: CheckM
[2023-03-19 01:50:21,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33770/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33770/checkm_input OceanDNA-b33770/checkm_result
[2023-03-19 01:50:36,593] [INFO] Task succeeded: CheckM
[2023-03-19 01:50:36,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.21%
Contamintation: 2.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 01:50:36,595] [INFO] ===== Completeness check finished =====
[2023-03-19 01:50:36,595] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:50:36,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33770/markers.fasta)
[2023-03-19 01:50:36,596] [INFO] Task started: Blastn
[2023-03-19 01:50:36,596] [INFO] Running command: blastn -query OceanDNA-b33770/markers.fasta -db /var/lib/cwl/stg438fa397-5f1a-465c-8bf7-2be531a29d92/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33770/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:37,367] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:37,368] [INFO] Selected 21 target genomes.
[2023-03-19 01:50:37,368] [INFO] Target genome list was writen to OceanDNA-b33770/target_genomes_gtdb.txt
[2023-03-19 01:50:37,382] [INFO] Task started: fastANI
[2023-03-19 01:50:37,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg94bbc994-e3fe-4185-a47e-9b31a1ad9e94/OceanDNA-b33770.fa --refList OceanDNA-b33770/target_genomes_gtdb.txt --output OceanDNA-b33770/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:50:42,635] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:42,639] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:50:42,639] [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_905181685.1	s__BACL14 sp905181685	87.5031	143	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182075.1	s__BACL14 sp905182075	80.8164	77	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018657165.1	s__BACL14 sp018657165	80.7526	145	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.24	99.09	0.82	0.76	15	-
GCA_018607785.1	s__BACL14 sp018607785	79.9441	151	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.17	98.94	0.86	0.81	5	-
--------------------------------------------------------------------------------
[2023-03-19 01:50:42,639] [INFO] GTDB search result was written to OceanDNA-b33770/result_gtdb.tsv
[2023-03-19 01:50:42,639] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:50:42,640] [INFO] DFAST_QC result json was written to OceanDNA-b33770/dqc_result.json
[2023-03-19 01:50:42,640] [INFO] DFAST_QC completed!
[2023-03-19 01:50:42,640] [INFO] Total running time: 0h0m41s