[2023-03-15 13:03:53,465] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,465] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg5496e4ba-e92a-4e0f-a7dc-dd66dec52f56/dqc_reference
[2023-03-15 13:03:54,671] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,672] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,672] [INFO] Running command: cat /var/lib/cwl/stg66e939b7-b3d1-4236-a0f3-e3923dc41732/OceanDNA-b26926.fa | prodigal -d OceanDNA-b26926/cds.fna -a OceanDNA-b26926/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:07,506] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:07,506] [INFO] Task started: HMMsearch
[2023-03-15 13:04:07,506] [INFO] Running command: hmmsearch --tblout OceanDNA-b26926/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5496e4ba-e92a-4e0f-a7dc-dd66dec52f56/dqc_reference/reference_markers.hmm OceanDNA-b26926/protein.faa > /dev/null
[2023-03-15 13:04:07,717] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:07,718] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg66e939b7-b3d1-4236-a0f3-e3923dc41732/OceanDNA-b26926.fa]
[2023-03-15 13:04:07,740] [INFO] Query marker FASTA was written to OceanDNA-b26926/markers.fasta
[2023-03-15 13:04:07,740] [INFO] Task started: Blastn
[2023-03-15 13:04:07,740] [INFO] Running command: blastn -query OceanDNA-b26926/markers.fasta -db /var/lib/cwl/stg5496e4ba-e92a-4e0f-a7dc-dd66dec52f56/dqc_reference/reference_markers.fasta -out OceanDNA-b26926/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:08,391] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:08,392] [INFO] Selected 9 target genomes.
[2023-03-15 13:04:08,392] [INFO] Target genome list was writen to OceanDNA-b26926/target_genomes.txt
[2023-03-15 13:04:08,398] [INFO] Task started: fastANI
[2023-03-15 13:04:08,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg66e939b7-b3d1-4236-a0f3-e3923dc41732/OceanDNA-b26926.fa --refList OceanDNA-b26926/target_genomes.txt --output OceanDNA-b26926/fastani_result.tsv --threads 1
[2023-03-15 13:04:14,889] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:14,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5496e4ba-e92a-4e0f-a7dc-dd66dec52f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:14,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5496e4ba-e92a-4e0f-a7dc-dd66dec52f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:14,896] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:14,896] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:04:14,896] [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
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	79.8455	337	619	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	79.8215	338	619	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	79.669	353	619	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.4862	239	619	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	77.7686	198	619	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	77.7592	199	619	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	77.69	190	619	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	77.5714	186	619	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	76.9449	138	619	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:04:14,897] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26926/tc_result.tsv
[2023-03-15 13:04:14,897] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:14,897] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:14,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5496e4ba-e92a-4e0f-a7dc-dd66dec52f56/dqc_reference/checkm_data
[2023-03-15 13:04:14,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:14,902] [INFO] Task started: CheckM
[2023-03-15 13:04:14,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26926/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26926/checkm_input OceanDNA-b26926/checkm_result
[2023-03-15 13:04:50,409] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:50,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:50,412] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:50,413] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:50,413] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26926/markers.fasta)
[2023-03-15 13:04:50,413] [INFO] Task started: Blastn
[2023-03-15 13:04:50,413] [INFO] Running command: blastn -query OceanDNA-b26926/markers.fasta -db /var/lib/cwl/stg5496e4ba-e92a-4e0f-a7dc-dd66dec52f56/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26926/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:51,348] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:51,349] [INFO] Selected 6 target genomes.
[2023-03-15 13:04:51,349] [INFO] Target genome list was writen to OceanDNA-b26926/target_genomes_gtdb.txt
[2023-03-15 13:04:51,407] [INFO] Task started: fastANI
[2023-03-15 13:04:51,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg66e939b7-b3d1-4236-a0f3-e3923dc41732/OceanDNA-b26926.fa --refList OceanDNA-b26926/target_genomes_gtdb.txt --output OceanDNA-b26926/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:04:56,596] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:56,601] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:04:56,601] [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
GCF_009789575.1	s__Stappia indica_A	98.3037	615	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003610575.1	s__Stappia sp003610575	92.1882	587	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_001696535.1	s__Stappia indica	92.1007	605	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_900185725.1	s__Stappia sp900185725	88.7944	558	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCA_002709505.1	s__Stappia sp002709505	80.819	328	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722295.1	s__Stappia sp002722295	80.2023	349	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	99.88	99.88	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:04:56,601] [INFO] GTDB search result was written to OceanDNA-b26926/result_gtdb.tsv
[2023-03-15 13:04:56,601] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:04:56,602] [INFO] DFAST_QC result json was written to OceanDNA-b26926/dqc_result.json
[2023-03-15 13:04:56,603] [INFO] DFAST_QC completed!
[2023-03-15 13:04:56,603] [INFO] Total running time: 0h1m3s