[2023-03-15 15:55:16,222] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,222] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,222] [INFO] DQC Reference Directory: /var/lib/cwl/stgd92a1d1b-f8c3-40c6-999c-ccc7f5767173/dqc_reference
[2023-03-15 15:55:17,919] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,920] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,920] [INFO] Running command: cat /var/lib/cwl/stgadb8e056-2a4d-4f79-87fa-16a9974764d2/OceanDNA-b4871.fa | prodigal -d OceanDNA-b4871/cds.fna -a OceanDNA-b4871/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:23,660] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:23,660] [INFO] Task started: HMMsearch
[2023-03-15 15:55:23,660] [INFO] Running command: hmmsearch --tblout OceanDNA-b4871/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd92a1d1b-f8c3-40c6-999c-ccc7f5767173/dqc_reference/reference_markers.hmm OceanDNA-b4871/protein.faa > /dev/null
[2023-03-15 15:55:23,832] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:23,833] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgadb8e056-2a4d-4f79-87fa-16a9974764d2/OceanDNA-b4871.fa]
[2023-03-15 15:55:23,842] [INFO] Query marker FASTA was written to OceanDNA-b4871/markers.fasta
[2023-03-15 15:55:23,842] [INFO] Task started: Blastn
[2023-03-15 15:55:23,842] [INFO] Running command: blastn -query OceanDNA-b4871/markers.fasta -db /var/lib/cwl/stgd92a1d1b-f8c3-40c6-999c-ccc7f5767173/dqc_reference/reference_markers.fasta -out OceanDNA-b4871/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:24,353] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:24,354] [INFO] Selected 30 target genomes.
[2023-03-15 15:55:24,354] [INFO] Target genome list was writen to OceanDNA-b4871/target_genomes.txt
[2023-03-15 15:55:24,375] [INFO] Task started: fastANI
[2023-03-15 15:55:24,375] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb8e056-2a4d-4f79-87fa-16a9974764d2/OceanDNA-b4871.fa --refList OceanDNA-b4871/target_genomes.txt --output OceanDNA-b4871/fastani_result.tsv --threads 1
[2023-03-15 15:55:39,502] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:39,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd92a1d1b-f8c3-40c6-999c-ccc7f5767173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:39,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd92a1d1b-f8c3-40c6-999c-ccc7f5767173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:39,503] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:39,503] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:55:39,503] [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
--------------------------------------------------------------------------------
[2023-03-15 15:55:39,503] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4871/tc_result.tsv
[2023-03-15 15:55:39,503] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:39,503] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:39,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd92a1d1b-f8c3-40c6-999c-ccc7f5767173/dqc_reference/checkm_data
[2023-03-15 15:55:39,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:39,508] [INFO] Task started: CheckM
[2023-03-15 15:55:39,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4871/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4871/checkm_input OceanDNA-b4871/checkm_result
[2023-03-15 15:55:59,533] [INFO] Task succeeded: CheckM
[2023-03-15 15:55:59,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:55:59,535] [INFO] ===== Completeness check finished =====
[2023-03-15 15:55:59,535] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:55:59,535] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4871/markers.fasta)
[2023-03-15 15:55:59,536] [INFO] Task started: Blastn
[2023-03-15 15:55:59,537] [INFO] Running command: blastn -query OceanDNA-b4871/markers.fasta -db /var/lib/cwl/stgd92a1d1b-f8c3-40c6-999c-ccc7f5767173/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4871/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:00,270] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:00,270] [INFO] Selected 23 target genomes.
[2023-03-15 15:56:00,271] [INFO] Target genome list was writen to OceanDNA-b4871/target_genomes_gtdb.txt
[2023-03-15 15:56:00,291] [INFO] Task started: fastANI
[2023-03-15 15:56:00,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb8e056-2a4d-4f79-87fa-16a9974764d2/OceanDNA-b4871.fa --refList OceanDNA-b4871/target_genomes_gtdb.txt --output OceanDNA-b4871/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:06,907] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:06,915] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:56:06,915] [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_002730985.1	s__BACL11 sp002730985	78.9814	122	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	97.22	97.22	0.84	0.84	2	-
GCA_002693745.1	s__BACL11 sp002693745	77.3675	95	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_002705205.1	s__GCA-2705205 sp002705205	77.3183	97	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2705205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	77.2132	94	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	77.0695	118	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181635.1	s__UWMA-0277 sp905181635	77.0486	57	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	77.0218	110	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_012960805.1	s__UWMA-0277 sp012960805	76.7796	91	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612305.1	s__UWMA-0277 sp905612305	76.7607	77	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683775.1	s__GCA-2683775 sp002683775	76.7222	50	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664745.1	s__UWMA-0277 sp018664745	76.6078	78	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645865.1	s__UWMA-0277 sp018645865	76.5879	62	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
GCA_002711125.1	s__GCA-2711125 sp002711125	76.4823	64	293	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:06,915] [INFO] GTDB search result was written to OceanDNA-b4871/result_gtdb.tsv
[2023-03-15 15:56:06,915] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:06,916] [INFO] DFAST_QC result json was written to OceanDNA-b4871/dqc_result.json
[2023-03-15 15:56:06,916] [INFO] DFAST_QC completed!
[2023-03-15 15:56:06,916] [INFO] Total running time: 0h0m51s