[2023-03-14 10:55:58,906] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,906] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg8745f418-c13f-42fc-9c43-e16a76971d1c/dqc_reference
[2023-03-14 10:56:00,679] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,680] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,680] [INFO] Running command: cat /var/lib/cwl/stg7d11b7de-423d-453c-b9f8-2bca9e339384/OceanDNA-b28098.fa | prodigal -d OceanDNA-b28098/cds.fna -a OceanDNA-b28098/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:14,850] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:14,850] [INFO] Task started: HMMsearch
[2023-03-14 10:56:14,850] [INFO] Running command: hmmsearch --tblout OceanDNA-b28098/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8745f418-c13f-42fc-9c43-e16a76971d1c/dqc_reference/reference_markers.hmm OceanDNA-b28098/protein.faa > /dev/null
[2023-03-14 10:56:15,084] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:15,085] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7d11b7de-423d-453c-b9f8-2bca9e339384/OceanDNA-b28098.fa]
[2023-03-14 10:56:15,106] [INFO] Query marker FASTA was written to OceanDNA-b28098/markers.fasta
[2023-03-14 10:56:15,106] [INFO] Task started: Blastn
[2023-03-14 10:56:15,106] [INFO] Running command: blastn -query OceanDNA-b28098/markers.fasta -db /var/lib/cwl/stg8745f418-c13f-42fc-9c43-e16a76971d1c/dqc_reference/reference_markers.fasta -out OceanDNA-b28098/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:15,684] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:15,685] [INFO] Selected 23 target genomes.
[2023-03-14 10:56:15,685] [INFO] Target genome list was writen to OceanDNA-b28098/target_genomes.txt
[2023-03-14 10:56:15,696] [INFO] Task started: fastANI
[2023-03-14 10:56:15,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d11b7de-423d-453c-b9f8-2bca9e339384/OceanDNA-b28098.fa --refList OceanDNA-b28098/target_genomes.txt --output OceanDNA-b28098/fastani_result.tsv --threads 1
[2023-03-14 10:56:31,257] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:31,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8745f418-c13f-42fc-9c43-e16a76971d1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:31,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8745f418-c13f-42fc-9c43-e16a76971d1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:31,261] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:31,261] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:31,261] [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
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.3301	89	756	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:31,261] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28098/tc_result.tsv
[2023-03-14 10:56:31,261] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:31,262] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:31,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8745f418-c13f-42fc-9c43-e16a76971d1c/dqc_reference/checkm_data
[2023-03-14 10:56:31,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:31,346] [INFO] Task started: CheckM
[2023-03-14 10:56:31,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28098/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28098/checkm_input OceanDNA-b28098/checkm_result
[2023-03-14 10:57:09,951] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:09,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:09,953] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:09,954] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:09,954] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28098/markers.fasta)
[2023-03-14 10:57:09,954] [INFO] Task started: Blastn
[2023-03-14 10:57:09,954] [INFO] Running command: blastn -query OceanDNA-b28098/markers.fasta -db /var/lib/cwl/stg8745f418-c13f-42fc-9c43-e16a76971d1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28098/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:10,888] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:10,889] [INFO] Selected 19 target genomes.
[2023-03-14 10:57:10,889] [INFO] Target genome list was writen to OceanDNA-b28098/target_genomes_gtdb.txt
[2023-03-14 10:57:10,907] [INFO] Task started: fastANI
[2023-03-14 10:57:10,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d11b7de-423d-453c-b9f8-2bca9e339384/OceanDNA-b28098.fa --refList OceanDNA-b28098/target_genomes_gtdb.txt --output OceanDNA-b28098/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:22,623] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:22,630] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:57:22,630] [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_013042895.1	s__Boseongicola sp013042895	77.4139	93	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	98.28	98.28	0.61	0.61	2	-
GCA_013042105.1	s__Boseongicola sp013042105	77.3952	148	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.16	99.16	0.85	0.85	2	-
GCF_900184815.1	s__Boseongicola aestuarii	77.1675	193	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014075275.1	s__Boseongicola sp014075275	76.5307	93	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.87	99.87	0.99	0.99	2	-
GCA_009830125.1	s__GH1-50 sp009830125	76.3301	89	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002465.1	s__JABDJO01 sp013002465	76.3124	67	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210165.1	s__CAU-1492 sp002210165	76.2214	54	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103375.1	s__WLWX01 sp012103375	76.0445	52	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WLWX01	95.0	99.99	99.98	0.99	0.99	3	-
GCF_013034685.1	s__Ruegeria lacuscaerulensis_B	75.941	50	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.87	97.79	0.94	0.94	3	-
GCF_003148765.1	s__Silicimonas algicola	75.9276	51	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001078595.1	s__Rhodobacter_B lobularis	75.7024	52	756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:22,630] [INFO] GTDB search result was written to OceanDNA-b28098/result_gtdb.tsv
[2023-03-14 10:57:22,630] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:22,631] [INFO] DFAST_QC result json was written to OceanDNA-b28098/dqc_result.json
[2023-03-14 10:57:22,631] [INFO] DFAST_QC completed!
[2023-03-14 10:57:22,631] [INFO] Total running time: 0h1m24s