[2023-03-16 07:28:29,976] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:29,976] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:29,976] [INFO] DQC Reference Directory: /var/lib/cwl/stg5662c57e-02a7-4850-a4dc-2c988bad6546/dqc_reference
[2023-03-16 07:28:31,105] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,105] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,105] [INFO] Running command: cat /var/lib/cwl/stg6c76fb55-2728-4626-adc4-92cf7a455a16/OceanDNA-b41999.fa | prodigal -d OceanDNA-b41999/cds.fna -a OceanDNA-b41999/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:34,484] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:34,484] [INFO] Task started: HMMsearch
[2023-03-16 07:28:34,484] [INFO] Running command: hmmsearch --tblout OceanDNA-b41999/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5662c57e-02a7-4850-a4dc-2c988bad6546/dqc_reference/reference_markers.hmm OceanDNA-b41999/protein.faa > /dev/null
[2023-03-16 07:28:34,635] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:34,636] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6c76fb55-2728-4626-adc4-92cf7a455a16/OceanDNA-b41999.fa]
[2023-03-16 07:28:34,643] [INFO] Query marker FASTA was written to OceanDNA-b41999/markers.fasta
[2023-03-16 07:28:34,644] [INFO] Task started: Blastn
[2023-03-16 07:28:34,644] [INFO] Running command: blastn -query OceanDNA-b41999/markers.fasta -db /var/lib/cwl/stg5662c57e-02a7-4850-a4dc-2c988bad6546/dqc_reference/reference_markers.fasta -out OceanDNA-b41999/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:35,162] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:35,163] [INFO] Selected 15 target genomes.
[2023-03-16 07:28:35,164] [INFO] Target genome list was writen to OceanDNA-b41999/target_genomes.txt
[2023-03-16 07:28:35,175] [INFO] Task started: fastANI
[2023-03-16 07:28:35,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c76fb55-2728-4626-adc4-92cf7a455a16/OceanDNA-b41999.fa --refList OceanDNA-b41999/target_genomes.txt --output OceanDNA-b41999/fastani_result.tsv --threads 1
[2023-03-16 07:28:41,962] [INFO] Task succeeded: fastANI
[2023-03-16 07:28:41,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5662c57e-02a7-4850-a4dc-2c988bad6546/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:28:41,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5662c57e-02a7-4850-a4dc-2c988bad6546/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:28:41,963] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:28:41,963] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:28:41,963] [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 07:28:41,964] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41999/tc_result.tsv
[2023-03-16 07:28:41,964] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:28:41,964] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:28:41,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5662c57e-02a7-4850-a4dc-2c988bad6546/dqc_reference/checkm_data
[2023-03-16 07:28:41,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:28:41,971] [INFO] Task started: CheckM
[2023-03-16 07:28:41,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41999/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41999/checkm_input OceanDNA-b41999/checkm_result
[2023-03-16 07:28:57,446] [INFO] Task succeeded: CheckM
[2023-03-16 07:28:57,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:28:57,450] [INFO] ===== Completeness check finished =====
[2023-03-16 07:28:57,450] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:28:57,450] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41999/markers.fasta)
[2023-03-16 07:28:57,452] [INFO] Task started: Blastn
[2023-03-16 07:28:57,452] [INFO] Running command: blastn -query OceanDNA-b41999/markers.fasta -db /var/lib/cwl/stg5662c57e-02a7-4850-a4dc-2c988bad6546/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41999/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:58,709] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:58,712] [INFO] Selected 16 target genomes.
[2023-03-16 07:28:58,712] [INFO] Target genome list was writen to OceanDNA-b41999/target_genomes_gtdb.txt
[2023-03-16 07:28:58,867] [INFO] Task started: fastANI
[2023-03-16 07:28:58,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c76fb55-2728-4626-adc4-92cf7a455a16/OceanDNA-b41999.fa --refList OceanDNA-b41999/target_genomes_gtdb.txt --output OceanDNA-b41999/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:29:02,228] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:02,237] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:29:02,237] [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_902515155.1	s__SCGC-AAA076-P13 sp902515155	96.8406	174	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	78.2951	96	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_902635645.1	s__SCGC-AAA076-P13 sp902635645	77.8224	69	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.13	97.13	0.67	0.67	2	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	77.7569	75	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_905478035.1	s__SCGC-AAA076-P13 sp905478035	77.656	93	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	77.6025	90	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_018607365.1	s__SCGC-AAA076-P13 sp018607365	77.5958	94	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	77.5876	91	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558375.1	s__SCGC-AAA076-P13 sp902558375	77.5591	67	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902610905.1	s__SCGC-AAA076-P13 sp902610905	77.5214	66	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591565.1	s__SCGC-AAA076-P13 sp902591565	77.4383	74	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558095.1	s__SAR86A sp902558095	77.1341	59	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	77.1003	62	227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:29:02,238] [INFO] GTDB search result was written to OceanDNA-b41999/result_gtdb.tsv
[2023-03-16 07:29:02,239] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:29:02,242] [INFO] DFAST_QC result json was written to OceanDNA-b41999/dqc_result.json
[2023-03-16 07:29:02,242] [INFO] DFAST_QC completed!
[2023-03-16 07:29:02,242] [INFO] Total running time: 0h0m32s