[2023-03-16 08:59:43,908] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:59:43,908] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:59:43,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7192f74-9257-40a9-a507-2b651e252516/dqc_reference
[2023-03-16 08:59:45,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:59:45,387] [INFO] Task started: Prodigal
[2023-03-16 08:59:45,387] [INFO] Running command: cat /var/lib/cwl/stgd57069ce-9c16-4c9e-8c40-15ccbe1480d2/OceanDNA-b5264.fa | prodigal -d OceanDNA-b5264/cds.fna -a OceanDNA-b5264/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:59:57,117] [INFO] Task succeeded: Prodigal
[2023-03-16 08:59:57,117] [INFO] Task started: HMMsearch
[2023-03-16 08:59:57,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b5264/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7192f74-9257-40a9-a507-2b651e252516/dqc_reference/reference_markers.hmm OceanDNA-b5264/protein.faa > /dev/null
[2023-03-16 08:59:57,302] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:59:57,303] [INFO] Found 6/6 markers.
[2023-03-16 08:59:57,318] [INFO] Query marker FASTA was written to OceanDNA-b5264/markers.fasta
[2023-03-16 08:59:57,319] [INFO] Task started: Blastn
[2023-03-16 08:59:57,319] [INFO] Running command: blastn -query OceanDNA-b5264/markers.fasta -db /var/lib/cwl/stgd7192f74-9257-40a9-a507-2b651e252516/dqc_reference/reference_markers.fasta -out OceanDNA-b5264/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:59:57,864] [INFO] Task succeeded: Blastn
[2023-03-16 08:59:57,864] [INFO] Selected 40 target genomes.
[2023-03-16 08:59:57,865] [INFO] Target genome list was writen to OceanDNA-b5264/target_genomes.txt
[2023-03-16 08:59:57,888] [INFO] Task started: fastANI
[2023-03-16 08:59:57,888] [INFO] Running command: fastANI --query /var/lib/cwl/stgd57069ce-9c16-4c9e-8c40-15ccbe1480d2/OceanDNA-b5264.fa --refList OceanDNA-b5264/target_genomes.txt --output OceanDNA-b5264/fastani_result.tsv --threads 1
[2023-03-16 09:00:20,848] [INFO] Task succeeded: fastANI
[2023-03-16 09:00:20,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7192f74-9257-40a9-a507-2b651e252516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:00:20,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7192f74-9257-40a9-a507-2b651e252516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:00:20,851] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:00:20,851] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:00:20,851] [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	75.838	52	594	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:00:20,852] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5264/tc_result.tsv
[2023-03-16 09:00:20,852] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:00:20,852] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:00:20,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7192f74-9257-40a9-a507-2b651e252516/dqc_reference/checkm_data
[2023-03-16 09:00:20,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:00:20,918] [INFO] Task started: CheckM
[2023-03-16 09:00:20,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5264/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5264/checkm_input OceanDNA-b5264/checkm_result
[2023-03-16 09:00:54,436] [INFO] Task succeeded: CheckM
[2023-03-16 09:00:54,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 09:00:54,476] [INFO] ===== Completeness check finished =====
[2023-03-16 09:00:54,477] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:00:54,477] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5264/markers.fasta)
[2023-03-16 09:00:54,478] [INFO] Task started: Blastn
[2023-03-16 09:00:54,478] [INFO] Running command: blastn -query OceanDNA-b5264/markers.fasta -db /var/lib/cwl/stgd7192f74-9257-40a9-a507-2b651e252516/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5264/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:00:55,250] [INFO] Task succeeded: Blastn
[2023-03-16 09:00:55,251] [INFO] Selected 34 target genomes.
[2023-03-16 09:00:55,251] [INFO] Target genome list was writen to OceanDNA-b5264/target_genomes_gtdb.txt
[2023-03-16 09:00:55,300] [INFO] Task started: fastANI
[2023-03-16 09:00:55,300] [INFO] Running command: fastANI --query /var/lib/cwl/stgd57069ce-9c16-4c9e-8c40-15ccbe1480d2/OceanDNA-b5264.fa --refList OceanDNA-b5264/target_genomes_gtdb.txt --output OceanDNA-b5264/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:01:10,426] [INFO] Task succeeded: fastANI
[2023-03-16 09:01:10,431] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:01:10,431] [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_903899795.1	s__CAIUKX01 sp903899795	77.1807	71	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178305.1	s__CAIUKX01 sp016178305	77.0831	130	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984635.1	s__M0103 sp017984635	76.9471	83	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885545.1	s__M0103 sp009885545	76.1651	75	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883325.1	s__UBA952 sp018883325	76.0261	60	594	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	75.8629	51	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183815.1	s__M2408 sp016183815	75.6516	56	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M2408	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:01:10,431] [INFO] GTDB search result was written to OceanDNA-b5264/result_gtdb.tsv
[2023-03-16 09:01:10,432] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:01:10,432] [INFO] DFAST_QC result json was written to OceanDNA-b5264/dqc_result.json
[2023-03-16 09:01:10,432] [INFO] DFAST_QC completed!
[2023-03-16 09:01:10,433] [INFO] Total running time: 0h1m27s