[2023-03-17 05:01:06,439] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,439] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg874788c9-194c-40a7-b9b7-249d940d0731/dqc_reference
[2023-03-17 05:01:07,998] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:07,999] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,000] [INFO] Running command: cat /var/lib/cwl/stgadb8ee4a-5c54-43f5-8b4a-87475faf60c8/OceanDNA-b30596.fa | prodigal -d OceanDNA-b30596/cds.fna -a OceanDNA-b30596/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:20,920] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:20,920] [INFO] Task started: HMMsearch
[2023-03-17 05:01:20,920] [INFO] Running command: hmmsearch --tblout OceanDNA-b30596/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg874788c9-194c-40a7-b9b7-249d940d0731/dqc_reference/reference_markers.hmm OceanDNA-b30596/protein.faa > /dev/null
[2023-03-17 05:01:21,089] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:21,090] [INFO] Found 6/6 markers.
[2023-03-17 05:01:21,104] [INFO] Query marker FASTA was written to OceanDNA-b30596/markers.fasta
[2023-03-17 05:01:21,104] [INFO] Task started: Blastn
[2023-03-17 05:01:21,104] [INFO] Running command: blastn -query OceanDNA-b30596/markers.fasta -db /var/lib/cwl/stg874788c9-194c-40a7-b9b7-249d940d0731/dqc_reference/reference_markers.fasta -out OceanDNA-b30596/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:21,712] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:21,713] [INFO] Selected 32 target genomes.
[2023-03-17 05:01:21,713] [INFO] Target genome list was writen to OceanDNA-b30596/target_genomes.txt
[2023-03-17 05:01:21,728] [INFO] Task started: fastANI
[2023-03-17 05:01:21,728] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb8ee4a-5c54-43f5-8b4a-87475faf60c8/OceanDNA-b30596.fa --refList OceanDNA-b30596/target_genomes.txt --output OceanDNA-b30596/fastani_result.tsv --threads 1
[2023-03-17 05:01:40,045] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:40,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg874788c9-194c-40a7-b9b7-249d940d0731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:40,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg874788c9-194c-40a7-b9b7-249d940d0731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:40,049] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:01:40,049] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:01:40,049] [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
Pseudorhodobacter aquimaris	strain=KCTC 23043	GCA_001202025.1	687412	687412	type	True	76.2949	58	695	95	below_threshold
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	76.1305	70	695	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:01:40,049] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30596/tc_result.tsv
[2023-03-17 05:01:40,049] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:40,049] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:40,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg874788c9-194c-40a7-b9b7-249d940d0731/dqc_reference/checkm_data
[2023-03-17 05:01:40,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:40,054] [INFO] Task started: CheckM
[2023-03-17 05:01:40,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30596/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30596/checkm_input OceanDNA-b30596/checkm_result
[2023-03-17 05:02:15,693] [INFO] Task succeeded: CheckM
[2023-03-17 05:02:15,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:02:15,696] [INFO] ===== Completeness check finished =====
[2023-03-17 05:02:15,696] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:02:15,696] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30596/markers.fasta)
[2023-03-17 05:02:15,696] [INFO] Task started: Blastn
[2023-03-17 05:02:15,696] [INFO] Running command: blastn -query OceanDNA-b30596/markers.fasta -db /var/lib/cwl/stg874788c9-194c-40a7-b9b7-249d940d0731/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30596/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:02:16,724] [INFO] Task succeeded: Blastn
[2023-03-17 05:02:16,725] [INFO] Selected 28 target genomes.
[2023-03-17 05:02:16,725] [INFO] Target genome list was writen to OceanDNA-b30596/target_genomes_gtdb.txt
[2023-03-17 05:02:17,255] [INFO] Task started: fastANI
[2023-03-17 05:02:17,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb8ee4a-5c54-43f5-8b4a-87475faf60c8/OceanDNA-b30596.fa --refList OceanDNA-b30596/target_genomes_gtdb.txt --output OceanDNA-b30596/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:02:31,613] [INFO] Task succeeded: fastANI
[2023-03-17 05:02:31,619] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:02:31,619] [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_003536295.1	s__UBA10365 sp003536295	97.9071	435	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA10365	95.0	98.23	97.66	0.75	0.66	6	conclusive
GCF_005234135.1	s__Pseudorhodobacter turbinis	76.3038	69	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001202025.1	s__Pseudorhodobacter aquimaris	76.2949	58	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420745.1	s__Pseudorhodobacter ferrugineus	76.1866	83	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001202035.1	s__Pseudorhodobacter wandonensis	76.1305	70	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991405.1	s__Pseudorhodobacter sp003991405	76.0441	73	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828855.1	s__Cypionkella sp001828855	75.8517	51	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	99.95	99.91	0.99	0.97	3	-
GCA_903845215.1	s__CYK-10 sp903845215	75.7197	79	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CYK-10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:02:31,619] [INFO] GTDB search result was written to OceanDNA-b30596/result_gtdb.tsv
[2023-03-17 05:02:31,619] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:02:31,620] [INFO] DFAST_QC result json was written to OceanDNA-b30596/dqc_result.json
[2023-03-17 05:02:31,620] [INFO] DFAST_QC completed!
[2023-03-17 05:02:31,620] [INFO] Total running time: 0h1m25s