[2023-03-16 10:57:32,927] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:57:32,927] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:57:32,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg44832e7c-c939-4a03-9d72-f3003b9c1b38/dqc_reference
[2023-03-16 10:57:34,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:57:34,199] [INFO] Task started: Prodigal
[2023-03-16 10:57:34,199] [INFO] Running command: cat /var/lib/cwl/stgf1fbbb2c-09c4-472b-8692-c74319f31403/OceanDNA-b26009.fa | prodigal -d OceanDNA-b26009/cds.fna -a OceanDNA-b26009/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:57:44,579] [INFO] Task succeeded: Prodigal
[2023-03-16 10:57:44,579] [INFO] Task started: HMMsearch
[2023-03-16 10:57:44,579] [INFO] Running command: hmmsearch --tblout OceanDNA-b26009/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44832e7c-c939-4a03-9d72-f3003b9c1b38/dqc_reference/reference_markers.hmm OceanDNA-b26009/protein.faa > /dev/null
[2023-03-16 10:57:44,742] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:57:44,743] [INFO] Found 6/6 markers.
[2023-03-16 10:57:44,756] [INFO] Query marker FASTA was written to OceanDNA-b26009/markers.fasta
[2023-03-16 10:57:44,756] [INFO] Task started: Blastn
[2023-03-16 10:57:44,757] [INFO] Running command: blastn -query OceanDNA-b26009/markers.fasta -db /var/lib/cwl/stg44832e7c-c939-4a03-9d72-f3003b9c1b38/dqc_reference/reference_markers.fasta -out OceanDNA-b26009/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:57:45,314] [INFO] Task succeeded: Blastn
[2023-03-16 10:57:45,315] [INFO] Selected 25 target genomes.
[2023-03-16 10:57:45,316] [INFO] Target genome list was writen to OceanDNA-b26009/target_genomes.txt
[2023-03-16 10:57:45,341] [INFO] Task started: fastANI
[2023-03-16 10:57:45,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1fbbb2c-09c4-472b-8692-c74319f31403/OceanDNA-b26009.fa --refList OceanDNA-b26009/target_genomes.txt --output OceanDNA-b26009/fastani_result.tsv --threads 1
[2023-03-16 10:58:01,547] [INFO] Task succeeded: fastANI
[2023-03-16 10:58:01,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44832e7c-c939-4a03-9d72-f3003b9c1b38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:58:01,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44832e7c-c939-4a03-9d72-f3003b9c1b38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:58:01,548] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:58:01,548] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:58:01,548] [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 10:58:01,549] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26009/tc_result.tsv
[2023-03-16 10:58:01,549] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:58:01,549] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:58:01,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44832e7c-c939-4a03-9d72-f3003b9c1b38/dqc_reference/checkm_data
[2023-03-16 10:58:01,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:58:01,760] [INFO] Task started: CheckM
[2023-03-16 10:58:01,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26009/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26009/checkm_input OceanDNA-b26009/checkm_result
[2023-03-16 10:58:26,810] [INFO] Task succeeded: CheckM
[2023-03-16 10:58:26,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:58:26,813] [INFO] ===== Completeness check finished =====
[2023-03-16 10:58:26,813] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:58:26,813] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26009/markers.fasta)
[2023-03-16 10:58:26,814] [INFO] Task started: Blastn
[2023-03-16 10:58:26,815] [INFO] Running command: blastn -query OceanDNA-b26009/markers.fasta -db /var/lib/cwl/stg44832e7c-c939-4a03-9d72-f3003b9c1b38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26009/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:58:28,018] [INFO] Task succeeded: Blastn
[2023-03-16 10:58:28,020] [INFO] Selected 29 target genomes.
[2023-03-16 10:58:28,020] [INFO] Target genome list was writen to OceanDNA-b26009/target_genomes_gtdb.txt
[2023-03-16 10:58:28,083] [INFO] Task started: fastANI
[2023-03-16 10:58:28,083] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1fbbb2c-09c4-472b-8692-c74319f31403/OceanDNA-b26009.fa --refList OceanDNA-b26009/target_genomes_gtdb.txt --output OceanDNA-b26009/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:58:42,638] [INFO] Task succeeded: fastANI
[2023-03-16 10:58:42,663] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:58:42,664] [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_016777705.1	s__AAA536-G10 sp016777705	94.0886	258	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	96.71	95.13	0.61	0.57	3	-
GCA_003283875.1	s__AAA536-G10 sp003283875	78.1474	104	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.33	95.28	0.67	0.61	3	-
GCA_000421325.1	s__AAA536-G10 sp000421325	77.9595	154	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278095.1	s__AAA536-G10 sp003278095	77.8322	171	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.84	95.67	0.90	0.81	3	-
GCA_000384615.1	s__AAA536-G10 sp000384615	77.7722	148	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282145.1	s__AAA536-G10 sp003282145	77.7678	156	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003282435.1	s__AAA536-G10 sp003282435	77.533	104	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592615.1	s__AAA536-G10 sp902592615	77.5126	104	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622875.1	s__AAA536-G10 sp902622875	77.5029	139	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595515.1	s__AAA536-G10 sp902595515	77.3685	122	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616615.1	s__AAA536-G10 sp902616615	77.3669	112	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558885.1	s__AAA536-G10 sp902558885	77.3587	138	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595145.1	s__AAA536-G10 sp902595145	77.3566	101	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529515.1	s__AAA536-G10 sp902529515	77.2453	101	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.18	97.18	0.52	0.52	2	-
GCA_902618025.1	s__AAA536-G10 sp902618025	77.2446	102	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619805.1	s__AAA536-G10 sp902619805	77.1855	137	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625215.1	s__AAA536-G10 sp902625215	77.1777	136	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593735.1	s__AAA536-G10 sp902593735	77.145	114	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583415.1	s__AAA536-G10 sp902583415	77.1358	91	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902530325.1	s__AAA536-G10 sp902530325	77.1189	107	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619615.1	s__AAA536-G10 sp902619615	77.0829	156	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000383115.1	s__AAA536-G10 sp000383115	77.0656	113	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537945.1	s__AAA536-G10 sp902537945	77.0356	151	377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:58:42,665] [INFO] GTDB search result was written to OceanDNA-b26009/result_gtdb.tsv
[2023-03-16 10:58:42,665] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:58:42,671] [INFO] DFAST_QC result json was written to OceanDNA-b26009/dqc_result.json
[2023-03-16 10:58:42,671] [INFO] DFAST_QC completed!
[2023-03-16 10:58:42,671] [INFO] Total running time: 0h1m10s