[2023-03-15 13:39:34,879] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:39:34,881] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:39:34,881] [INFO] DQC Reference Directory: /var/lib/cwl/stga852e6ec-c362-4b02-8354-518a9968ea8e/dqc_reference
[2023-03-15 13:39:37,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:39:37,047] [INFO] Task started: Prodigal
[2023-03-15 13:39:37,048] [INFO] Running command: cat /var/lib/cwl/stgc2e8a6b1-b87a-470d-914c-6914e2af8607/OceanDNA-b5304.fa | prodigal -d OceanDNA-b5304/cds.fna -a OceanDNA-b5304/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:39:53,489] [INFO] Task succeeded: Prodigal
[2023-03-15 13:39:53,489] [INFO] Task started: HMMsearch
[2023-03-15 13:39:53,489] [INFO] Running command: hmmsearch --tblout OceanDNA-b5304/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga852e6ec-c362-4b02-8354-518a9968ea8e/dqc_reference/reference_markers.hmm OceanDNA-b5304/protein.faa > /dev/null
[2023-03-15 13:39:53,675] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:39:53,675] [INFO] Found 6/6 markers.
[2023-03-15 13:39:53,699] [INFO] Query marker FASTA was written to OceanDNA-b5304/markers.fasta
[2023-03-15 13:39:53,699] [INFO] Task started: Blastn
[2023-03-15 13:39:53,699] [INFO] Running command: blastn -query OceanDNA-b5304/markers.fasta -db /var/lib/cwl/stga852e6ec-c362-4b02-8354-518a9968ea8e/dqc_reference/reference_markers.fasta -out OceanDNA-b5304/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:39:54,230] [INFO] Task succeeded: Blastn
[2023-03-15 13:39:54,235] [INFO] Selected 19 target genomes.
[2023-03-15 13:39:54,236] [INFO] Target genome list was writen to OceanDNA-b5304/target_genomes.txt
[2023-03-15 13:39:54,247] [INFO] Task started: fastANI
[2023-03-15 13:39:54,247] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2e8a6b1-b87a-470d-914c-6914e2af8607/OceanDNA-b5304.fa --refList OceanDNA-b5304/target_genomes.txt --output OceanDNA-b5304/fastani_result.tsv --threads 1
[2023-03-15 13:40:05,057] [INFO] Task succeeded: fastANI
[2023-03-15 13:40:05,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga852e6ec-c362-4b02-8354-518a9968ea8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:40:05,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga852e6ec-c362-4b02-8354-518a9968ea8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:40:05,061] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:40:05,061] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:40:05,061] [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
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.2801	65	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:40:05,063] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5304/tc_result.tsv
[2023-03-15 13:40:05,065] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:40:05,065] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:40:05,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga852e6ec-c362-4b02-8354-518a9968ea8e/dqc_reference/checkm_data
[2023-03-15 13:40:05,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:40:05,075] [INFO] Task started: CheckM
[2023-03-15 13:40:05,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5304/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5304/checkm_input OceanDNA-b5304/checkm_result
[2023-03-15 13:40:49,981] [INFO] Task succeeded: CheckM
[2023-03-15 13:40:49,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:40:50,212] [INFO] ===== Completeness check finished =====
[2023-03-15 13:40:50,212] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:40:50,213] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5304/markers.fasta)
[2023-03-15 13:40:50,214] [INFO] Task started: Blastn
[2023-03-15 13:40:50,214] [INFO] Running command: blastn -query OceanDNA-b5304/markers.fasta -db /var/lib/cwl/stga852e6ec-c362-4b02-8354-518a9968ea8e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5304/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:40:50,969] [INFO] Task succeeded: Blastn
[2023-03-15 13:40:50,972] [INFO] Selected 21 target genomes.
[2023-03-15 13:40:50,972] [INFO] Target genome list was writen to OceanDNA-b5304/target_genomes_gtdb.txt
[2023-03-15 13:40:51,071] [INFO] Task started: fastANI
[2023-03-15 13:40:51,071] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2e8a6b1-b87a-470d-914c-6914e2af8607/OceanDNA-b5304.fa --refList OceanDNA-b5304/target_genomes_gtdb.txt --output OceanDNA-b5304/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:41:03,558] [INFO] Task succeeded: fastANI
[2023-03-15 13:41:03,565] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:41:03,565] [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_002384725.1	s__UBA2040 sp002384725	99.4465	571	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA2040	95.0	99.28	99.28	0.79	0.79	2	conclusive
GCA_002332715.1	s__UBA2040 sp002332715	88.5018	447	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA2040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945495.1	s__M0103 sp903945495	77.1169	79	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
GCA_018825925.1	s__UBA2040 sp018825925	77.056	60	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA2040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002734065.2	s__UBA4466 sp002734065	76.89	54	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984635.1	s__M0103 sp017984635	76.7834	70	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983675.1	s__Fluviicola sp017983675	76.6844	51	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	99.86	99.86	0.97	0.97	2	-
GCA_016178305.1	s__CAIUKX01 sp016178305	76.5593	63	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883325.1	s__UBA952 sp018883325	76.287	63	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194605.1	s__Fluviicola taffensis	76.2801	65	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885545.1	s__M0103 sp009885545	75.9273	51	711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:41:03,568] [INFO] GTDB search result was written to OceanDNA-b5304/result_gtdb.tsv
[2023-03-15 13:41:03,570] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:41:03,574] [INFO] DFAST_QC result json was written to OceanDNA-b5304/dqc_result.json
[2023-03-15 13:41:03,574] [INFO] DFAST_QC completed!
[2023-03-15 13:41:03,574] [INFO] Total running time: 0h1m29s