[2023-03-16 11:00:14,502] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:00:14,502] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:00:14,502] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5da9512-6623-40af-976f-5fa19c86c000/dqc_reference
[2023-03-16 11:00:15,642] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:00:15,643] [INFO] Task started: Prodigal
[2023-03-16 11:00:15,643] [INFO] Running command: cat /var/lib/cwl/stg8773c381-bad6-404a-834a-321483b298ea/OceanDNA-b10760.fa | prodigal -d OceanDNA-b10760/cds.fna -a OceanDNA-b10760/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:00:36,310] [INFO] Task succeeded: Prodigal
[2023-03-16 11:00:36,310] [INFO] Task started: HMMsearch
[2023-03-16 11:00:36,310] [INFO] Running command: hmmsearch --tblout OceanDNA-b10760/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5da9512-6623-40af-976f-5fa19c86c000/dqc_reference/reference_markers.hmm OceanDNA-b10760/protein.faa > /dev/null
[2023-03-16 11:00:36,504] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:00:36,505] [INFO] Found 6/6 markers.
[2023-03-16 11:00:36,520] [INFO] Query marker FASTA was written to OceanDNA-b10760/markers.fasta
[2023-03-16 11:00:36,522] [INFO] Task started: Blastn
[2023-03-16 11:00:36,523] [INFO] Running command: blastn -query OceanDNA-b10760/markers.fasta -db /var/lib/cwl/stgd5da9512-6623-40af-976f-5fa19c86c000/dqc_reference/reference_markers.fasta -out OceanDNA-b10760/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:00:37,326] [INFO] Task succeeded: Blastn
[2023-03-16 11:00:37,328] [INFO] Selected 33 target genomes.
[2023-03-16 11:00:37,329] [INFO] Target genome list was writen to OceanDNA-b10760/target_genomes.txt
[2023-03-16 11:00:37,356] [INFO] Task started: fastANI
[2023-03-16 11:00:37,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg8773c381-bad6-404a-834a-321483b298ea/OceanDNA-b10760.fa --refList OceanDNA-b10760/target_genomes.txt --output OceanDNA-b10760/fastani_result.tsv --threads 1
[2023-03-16 11:01:07,330] [INFO] Task succeeded: fastANI
[2023-03-16 11:01:07,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5da9512-6623-40af-976f-5fa19c86c000/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:01:07,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5da9512-6623-40af-976f-5fa19c86c000/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:01:07,331] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:01:07,331] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 11:01:07,331] [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
--------------------------------------------------------------------------------
[2023-03-16 11:01:07,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10760/tc_result.tsv
[2023-03-16 11:01:07,333] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:01:07,333] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:01:07,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5da9512-6623-40af-976f-5fa19c86c000/dqc_reference/checkm_data
[2023-03-16 11:01:07,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:01:07,407] [INFO] Task started: CheckM
[2023-03-16 11:01:07,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10760/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10760/checkm_input OceanDNA-b10760/checkm_result
[2023-03-16 11:01:49,483] [INFO] Task succeeded: CheckM
[2023-03-16 11:01:49,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:01:49,488] [INFO] ===== Completeness check finished =====
[2023-03-16 11:01:49,488] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:01:49,488] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10760/markers.fasta)
[2023-03-16 11:01:49,489] [INFO] Task started: Blastn
[2023-03-16 11:01:49,489] [INFO] Running command: blastn -query OceanDNA-b10760/markers.fasta -db /var/lib/cwl/stgd5da9512-6623-40af-976f-5fa19c86c000/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10760/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:01:50,414] [INFO] Task succeeded: Blastn
[2023-03-16 11:01:50,418] [INFO] Selected 12 target genomes.
[2023-03-16 11:01:50,418] [INFO] Target genome list was writen to OceanDNA-b10760/target_genomes_gtdb.txt
[2023-03-16 11:01:50,427] [INFO] Task started: fastANI
[2023-03-16 11:01:50,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg8773c381-bad6-404a-834a-321483b298ea/OceanDNA-b10760.fa --refList OceanDNA-b10760/target_genomes_gtdb.txt --output OceanDNA-b10760/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:01:58,057] [INFO] Task succeeded: fastANI
[2023-03-16 11:01:58,063] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:01:58,063] [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_002171575.2	s__UBA724 sp002171575	93.7213	334	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723075.1	s__UBA724 sp002723075	89.4176	430	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.07	97.94	0.92	0.77	6	-
GCA_902536935.1	s__UBA724 sp902536935	89.3466	387	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	96.07	96.07	0.80	0.80	2	-
GCA_902586905.1	s__UBA724 sp902586905	81.0338	257	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862705.1	s__UBA7446 sp002862705	80.6575	64	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.06	98.27	0.87	0.83	14	-
GCA_902619855.1	s__UBA724 sp902619855	80.0606	237	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902631125.1	s__UBA724 sp902631125	79.8345	183	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430545.1	s__UBA724 sp002430545	79.4789	240	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.84	99.84	0.94	0.94	2	-
GCA_018672145.1	s__UBA724 sp018672145	78.679	138	519	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.13	99.13	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-16 11:01:58,064] [INFO] GTDB search result was written to OceanDNA-b10760/result_gtdb.tsv
[2023-03-16 11:01:58,066] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:01:58,068] [INFO] DFAST_QC result json was written to OceanDNA-b10760/dqc_result.json
[2023-03-16 11:01:58,068] [INFO] DFAST_QC completed!
[2023-03-16 11:01:58,069] [INFO] Total running time: 0h1m44s