[2023-03-19 04:43:18,684] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,684] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ab107e8-4558-4d3a-94c6-9068b9356f95/dqc_reference
[2023-03-19 04:43:19,805] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,806] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,806] [INFO] Running command: cat /var/lib/cwl/stg0e3806cb-5663-4b9c-8660-b02d3e9f89f0/OceanDNA-b1833.fa | prodigal -d OceanDNA-b1833/cds.fna -a OceanDNA-b1833/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:33,786] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:33,786] [INFO] Task started: HMMsearch
[2023-03-19 04:43:33,786] [INFO] Running command: hmmsearch --tblout OceanDNA-b1833/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ab107e8-4558-4d3a-94c6-9068b9356f95/dqc_reference/reference_markers.hmm OceanDNA-b1833/protein.faa > /dev/null
[2023-03-19 04:43:33,937] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:33,938] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0e3806cb-5663-4b9c-8660-b02d3e9f89f0/OceanDNA-b1833.fa]
[2023-03-19 04:43:33,952] [INFO] Query marker FASTA was written to OceanDNA-b1833/markers.fasta
[2023-03-19 04:43:33,954] [INFO] Task started: Blastn
[2023-03-19 04:43:33,954] [INFO] Running command: blastn -query OceanDNA-b1833/markers.fasta -db /var/lib/cwl/stg1ab107e8-4558-4d3a-94c6-9068b9356f95/dqc_reference/reference_markers.fasta -out OceanDNA-b1833/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:34,537] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:34,538] [INFO] Selected 16 target genomes.
[2023-03-19 04:43:34,538] [INFO] Target genome list was writen to OceanDNA-b1833/target_genomes.txt
[2023-03-19 04:43:34,549] [INFO] Task started: fastANI
[2023-03-19 04:43:34,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e3806cb-5663-4b9c-8660-b02d3e9f89f0/OceanDNA-b1833.fa --refList OceanDNA-b1833/target_genomes.txt --output OceanDNA-b1833/fastani_result.tsv --threads 1
[2023-03-19 04:43:47,883] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:47,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ab107e8-4558-4d3a-94c6-9068b9356f95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:47,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ab107e8-4558-4d3a-94c6-9068b9356f95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:47,887] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:47,888] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:43:47,888] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.9114	51	706	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.7233	111	706	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:43:47,934] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1833/tc_result.tsv
[2023-03-19 04:43:47,934] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:47,934] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:47,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ab107e8-4558-4d3a-94c6-9068b9356f95/dqc_reference/checkm_data
[2023-03-19 04:43:47,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:47,958] [INFO] Task started: CheckM
[2023-03-19 04:43:47,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1833/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1833/checkm_input OceanDNA-b1833/checkm_result
[2023-03-19 04:44:25,791] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:25,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:44:25,793] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:25,793] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:25,794] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1833/markers.fasta)
[2023-03-19 04:44:25,794] [INFO] Task started: Blastn
[2023-03-19 04:44:25,794] [INFO] Running command: blastn -query OceanDNA-b1833/markers.fasta -db /var/lib/cwl/stg1ab107e8-4558-4d3a-94c6-9068b9356f95/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1833/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:26,643] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:26,644] [INFO] Selected 8 target genomes.
[2023-03-19 04:44:26,644] [INFO] Target genome list was writen to OceanDNA-b1833/target_genomes_gtdb.txt
[2023-03-19 04:44:26,671] [INFO] Task started: fastANI
[2023-03-19 04:44:26,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e3806cb-5663-4b9c-8660-b02d3e9f89f0/OceanDNA-b1833.fa --refList OceanDNA-b1833/target_genomes_gtdb.txt --output OceanDNA-b1833/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:44:30,672] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:30,677] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:44:30,678] [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_005787345.1	s__F1-20-MAGs160 sp005787345	91.5187	559	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	96.08	96.08	0.84	0.84	2	-
GCA_009703275.1	s__F1-20-MAGs160 sp009703275	90.5478	438	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	98.87	98.58	0.79	0.77	4	-
GCA_903827085.1	s__F1-20-MAGs160 sp903827085	90.1528	390	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699125.1	s__F1-20-MAGs160 sp009699125	84.7973	430	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	99.35	99.30	0.87	0.87	3	-
GCA_016462055.1	s__F1-20-MAGs160 sp016462055	81.3717	314	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009700115.1	s__F1-20-MAGs160 sp009700115	80.831	336	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	99.37	98.87	0.88	0.85	10	-
GCA_903867185.1	s__F1-20-MAGs160 sp903867185	80.5934	381	706	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:44:30,678] [INFO] GTDB search result was written to OceanDNA-b1833/result_gtdb.tsv
[2023-03-19 04:44:30,678] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:44:30,679] [INFO] DFAST_QC result json was written to OceanDNA-b1833/dqc_result.json
[2023-03-19 04:44:30,679] [INFO] DFAST_QC completed!
[2023-03-19 04:44:30,679] [INFO] Total running time: 0h1m12s