[2023-03-16 09:50:49,972] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:50:49,974] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:50:49,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fe7083d-0dbe-4c27-8a7c-8e6b2444670e/dqc_reference
[2023-03-16 09:50:51,070] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:50:51,071] [INFO] Task started: Prodigal
[2023-03-16 09:50:51,071] [INFO] Running command: cat /var/lib/cwl/stgcb73d81c-bc5f-436f-a8bb-0ac8170c6dc7/OceanDNA-b6744.fa | prodigal -d OceanDNA-b6744/cds.fna -a OceanDNA-b6744/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:51:11,657] [INFO] Task succeeded: Prodigal
[2023-03-16 09:51:11,657] [INFO] Task started: HMMsearch
[2023-03-16 09:51:11,657] [INFO] Running command: hmmsearch --tblout OceanDNA-b6744/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fe7083d-0dbe-4c27-8a7c-8e6b2444670e/dqc_reference/reference_markers.hmm OceanDNA-b6744/protein.faa > /dev/null
[2023-03-16 09:51:11,840] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:51:11,841] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcb73d81c-bc5f-436f-a8bb-0ac8170c6dc7/OceanDNA-b6744.fa]
[2023-03-16 09:51:11,876] [INFO] Query marker FASTA was written to OceanDNA-b6744/markers.fasta
[2023-03-16 09:51:11,877] [INFO] Task started: Blastn
[2023-03-16 09:51:11,877] [INFO] Running command: blastn -query OceanDNA-b6744/markers.fasta -db /var/lib/cwl/stg7fe7083d-0dbe-4c27-8a7c-8e6b2444670e/dqc_reference/reference_markers.fasta -out OceanDNA-b6744/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:51:12,434] [INFO] Task succeeded: Blastn
[2023-03-16 09:51:12,440] [INFO] Selected 20 target genomes.
[2023-03-16 09:51:12,441] [INFO] Target genome list was writen to OceanDNA-b6744/target_genomes.txt
[2023-03-16 09:51:12,453] [INFO] Task started: fastANI
[2023-03-16 09:51:12,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb73d81c-bc5f-436f-a8bb-0ac8170c6dc7/OceanDNA-b6744.fa --refList OceanDNA-b6744/target_genomes.txt --output OceanDNA-b6744/fastani_result.tsv --threads 1
[2023-03-16 09:51:24,294] [INFO] Task succeeded: fastANI
[2023-03-16 09:51:24,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fe7083d-0dbe-4c27-8a7c-8e6b2444670e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:51:24,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fe7083d-0dbe-4c27-8a7c-8e6b2444670e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:51:24,302] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:51:24,303] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:51:24,303] [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
Dokdonia donghaensis	strain=DSW-1	GCA_001653755.1	326320	326320	type	True	76.7705	142	996	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_000769435.1	326320	326320	type	True	76.7352	146	996	95	below_threshold
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	76.7121	221	996	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	76.7094	220	996	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.6498	50	996	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	76.136	57	996	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	76.0953	62	996	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	75.9968	65	996	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	75.9694	56	996	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	75.9059	78	996	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.846	86	996	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:51:24,306] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6744/tc_result.tsv
[2023-03-16 09:51:24,309] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:51:24,309] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:51:24,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fe7083d-0dbe-4c27-8a7c-8e6b2444670e/dqc_reference/checkm_data
[2023-03-16 09:51:24,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:51:24,316] [INFO] Task started: CheckM
[2023-03-16 09:51:24,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6744/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6744/checkm_input OceanDNA-b6744/checkm_result
[2023-03-16 09:52:17,266] [INFO] Task succeeded: CheckM
[2023-03-16 09:52:17,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:52:17,327] [INFO] ===== Completeness check finished =====
[2023-03-16 09:52:17,327] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:52:17,327] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6744/markers.fasta)
[2023-03-16 09:52:17,328] [INFO] Task started: Blastn
[2023-03-16 09:52:17,328] [INFO] Running command: blastn -query OceanDNA-b6744/markers.fasta -db /var/lib/cwl/stg7fe7083d-0dbe-4c27-8a7c-8e6b2444670e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6744/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:52:18,131] [INFO] Task succeeded: Blastn
[2023-03-16 09:52:18,139] [INFO] Selected 21 target genomes.
[2023-03-16 09:52:18,139] [INFO] Target genome list was writen to OceanDNA-b6744/target_genomes_gtdb.txt
[2023-03-16 09:52:18,241] [INFO] Task started: fastANI
[2023-03-16 09:52:18,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb73d81c-bc5f-436f-a8bb-0ac8170c6dc7/OceanDNA-b6744.fa --refList OceanDNA-b6744/target_genomes_gtdb.txt --output OceanDNA-b6744/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:52:29,684] [INFO] Task succeeded: fastANI
[2023-03-16 09:52:29,693] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:52:29,693] [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_002712765.1	s__Dokdonia sp002712765	77.8131	196	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	99.61	99.61	0.82	0.82	2	-
GCF_000355805.1	s__Dokdonia sp000355805	77.1667	136	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095655.1	s__Dokdonia sp003095655	76.9915	152	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653755.1	s__Dokdonia donghaensis	76.7706	142	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	97.85	95.71	0.96	0.91	3	-
GCF_007827465.1	s__Dokdonia sp007827465	76.7243	126	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188275.1	s__Dokdonia pacifica	76.7218	219	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000212355.1	s__Dokdonia sp000212355	76.6887	158	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	98.49	98.49	0.97	0.97	2	-
GCF_900104785.1	s__Psychroserpens sp900104785	76.2957	50	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900112395.1	s__Algibacter lectus	76.0269	70	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_014764305.1	s__Mesoflavibacter profundi	75.9968	65	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	75.9876	56	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086205.1	s__Algorimicrobium myxarmorum	75.9521	55	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	75.9276	92	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	75.8853	69	996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:52:29,696] [INFO] GTDB search result was written to OceanDNA-b6744/result_gtdb.tsv
[2023-03-16 09:52:29,700] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:52:29,705] [INFO] DFAST_QC result json was written to OceanDNA-b6744/dqc_result.json
[2023-03-16 09:52:29,705] [INFO] DFAST_QC completed!
[2023-03-16 09:52:29,705] [INFO] Total running time: 0h1m40s