[2023-03-17 07:28:31,297] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,297] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cbb0f66-6304-4c0f-ae9a-cb80bb189dd2/dqc_reference
[2023-03-17 07:28:33,081] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,081] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,081] [INFO] Running command: cat /var/lib/cwl/stgae86efc5-f743-48fb-9df1-482d6b47740d/OceanDNA-b8576.fa | prodigal -d OceanDNA-b8576/cds.fna -a OceanDNA-b8576/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:38,998] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:38,998] [INFO] Task started: HMMsearch
[2023-03-17 07:28:38,998] [INFO] Running command: hmmsearch --tblout OceanDNA-b8576/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cbb0f66-6304-4c0f-ae9a-cb80bb189dd2/dqc_reference/reference_markers.hmm OceanDNA-b8576/protein.faa > /dev/null
[2023-03-17 07:28:39,164] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:39,165] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgae86efc5-f743-48fb-9df1-482d6b47740d/OceanDNA-b8576.fa]
[2023-03-17 07:28:39,174] [INFO] Query marker FASTA was written to OceanDNA-b8576/markers.fasta
[2023-03-17 07:28:39,174] [INFO] Task started: Blastn
[2023-03-17 07:28:39,174] [INFO] Running command: blastn -query OceanDNA-b8576/markers.fasta -db /var/lib/cwl/stg4cbb0f66-6304-4c0f-ae9a-cb80bb189dd2/dqc_reference/reference_markers.fasta -out OceanDNA-b8576/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:39,759] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:39,760] [INFO] Selected 28 target genomes.
[2023-03-17 07:28:39,760] [INFO] Target genome list was writen to OceanDNA-b8576/target_genomes.txt
[2023-03-17 07:28:39,778] [INFO] Task started: fastANI
[2023-03-17 07:28:39,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgae86efc5-f743-48fb-9df1-482d6b47740d/OceanDNA-b8576.fa --refList OceanDNA-b8576/target_genomes.txt --output OceanDNA-b8576/fastani_result.tsv --threads 1
[2023-03-17 07:28:54,234] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:54,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cbb0f66-6304-4c0f-ae9a-cb80bb189dd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:54,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cbb0f66-6304-4c0f-ae9a-cb80bb189dd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:54,235] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:54,235] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:28:54,235] [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
--------------------------------------------------------------------------------
[2023-03-17 07:28:54,235] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8576/tc_result.tsv
[2023-03-17 07:28:54,236] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:54,236] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:54,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cbb0f66-6304-4c0f-ae9a-cb80bb189dd2/dqc_reference/checkm_data
[2023-03-17 07:28:54,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:54,241] [INFO] Task started: CheckM
[2023-03-17 07:28:54,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8576/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8576/checkm_input OceanDNA-b8576/checkm_result
[2023-03-17 07:29:14,836] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:14,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:14,839] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:14,839] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:14,839] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8576/markers.fasta)
[2023-03-17 07:29:14,839] [INFO] Task started: Blastn
[2023-03-17 07:29:14,839] [INFO] Running command: blastn -query OceanDNA-b8576/markers.fasta -db /var/lib/cwl/stg4cbb0f66-6304-4c0f-ae9a-cb80bb189dd2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8576/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:15,626] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:15,627] [INFO] Selected 9 target genomes.
[2023-03-17 07:29:15,627] [INFO] Target genome list was writen to OceanDNA-b8576/target_genomes_gtdb.txt
[2023-03-17 07:29:15,758] [INFO] Task started: fastANI
[2023-03-17 07:29:15,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgae86efc5-f743-48fb-9df1-482d6b47740d/OceanDNA-b8576.fa --refList OceanDNA-b8576/target_genomes_gtdb.txt --output OceanDNA-b8576/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:17,734] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:17,740] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:29:17,740] [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_002457075.1	s__MED-G11 sp002457075	99.0633	221	317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	conclusive
GCA_014239665.1	s__MED-G11 sp014239665	90.9977	259	317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_018646865.1	s__MED-G11 sp014239615	83.9638	256	317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	-
GCA_902509805.1	s__MED-G11 sp902509805	83.7756	145	317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
GCA_004214015.1	s__MED-G11 sp004214015	83.4059	187	317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	-
GCA_016777325.1	s__MED-G11 sp016777325	83.0397	170	317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514615.1	s__MED-G11 sp902514615	82.7951	200	317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516925.1	s__MED-G11 sp902516925	80.266	167	317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905380995.1	s__MED-G11 sp905380995	78.6953	172	317	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:17,740] [INFO] GTDB search result was written to OceanDNA-b8576/result_gtdb.tsv
[2023-03-17 07:29:17,740] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:17,741] [INFO] DFAST_QC result json was written to OceanDNA-b8576/dqc_result.json
[2023-03-17 07:29:17,741] [INFO] DFAST_QC completed!
[2023-03-17 07:29:17,741] [INFO] Total running time: 0h0m46s