[2023-03-19 01:12:15,643] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:12:15,643] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:12:15,643] [INFO] DQC Reference Directory: /var/lib/cwl/stgec187f43-0590-46c4-9a20-e0ba6c0a6e21/dqc_reference
[2023-03-19 01:12:16,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:12:16,747] [INFO] Task started: Prodigal
[2023-03-19 01:12:16,747] [INFO] Running command: cat /var/lib/cwl/stgdcaa3824-d1f2-45f1-8e2d-b502123fd56c/OceanDNA-b18120.fa | prodigal -d OceanDNA-b18120/cds.fna -a OceanDNA-b18120/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:12:20,235] [INFO] Task succeeded: Prodigal
[2023-03-19 01:12:20,235] [INFO] Task started: HMMsearch
[2023-03-19 01:12:20,235] [INFO] Running command: hmmsearch --tblout OceanDNA-b18120/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec187f43-0590-46c4-9a20-e0ba6c0a6e21/dqc_reference/reference_markers.hmm OceanDNA-b18120/protein.faa > /dev/null
[2023-03-19 01:12:20,368] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:12:20,368] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdcaa3824-d1f2-45f1-8e2d-b502123fd56c/OceanDNA-b18120.fa]
[2023-03-19 01:12:20,375] [INFO] Query marker FASTA was written to OceanDNA-b18120/markers.fasta
[2023-03-19 01:12:20,376] [INFO] Task started: Blastn
[2023-03-19 01:12:20,376] [INFO] Running command: blastn -query OceanDNA-b18120/markers.fasta -db /var/lib/cwl/stgec187f43-0590-46c4-9a20-e0ba6c0a6e21/dqc_reference/reference_markers.fasta -out OceanDNA-b18120/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:22,347] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:22,348] [INFO] Selected 12 target genomes.
[2023-03-19 01:12:22,348] [INFO] Target genome list was writen to OceanDNA-b18120/target_genomes.txt
[2023-03-19 01:12:22,361] [INFO] Task started: fastANI
[2023-03-19 01:12:22,361] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcaa3824-d1f2-45f1-8e2d-b502123fd56c/OceanDNA-b18120.fa --refList OceanDNA-b18120/target_genomes.txt --output OceanDNA-b18120/fastani_result.tsv --threads 1
[2023-03-19 01:12:26,722] [INFO] Task succeeded: fastANI
[2023-03-19 01:12:26,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec187f43-0590-46c4-9a20-e0ba6c0a6e21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:12:26,723] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec187f43-0590-46c4-9a20-e0ba6c0a6e21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:12:26,723] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:12:26,723] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:12:26,723] [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
--------------------------------------------------------------------------------
[2023-03-19 01:12:26,723] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18120/tc_result.tsv
[2023-03-19 01:12:26,723] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:12:26,723] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:12:26,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec187f43-0590-46c4-9a20-e0ba6c0a6e21/dqc_reference/checkm_data
[2023-03-19 01:12:26,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:12:26,729] [INFO] Task started: CheckM
[2023-03-19 01:12:26,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18120/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18120/checkm_input OceanDNA-b18120/checkm_result
[2023-03-19 01:12:41,645] [INFO] Task succeeded: CheckM
[2023-03-19 01:12:41,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:12:41,647] [INFO] ===== Completeness check finished =====
[2023-03-19 01:12:41,647] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:12:41,647] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18120/markers.fasta)
[2023-03-19 01:12:41,649] [INFO] Task started: Blastn
[2023-03-19 01:12:41,649] [INFO] Running command: blastn -query OceanDNA-b18120/markers.fasta -db /var/lib/cwl/stgec187f43-0590-46c4-9a20-e0ba6c0a6e21/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18120/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:42,247] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:42,248] [INFO] Selected 13 target genomes.
[2023-03-19 01:12:42,249] [INFO] Target genome list was writen to OceanDNA-b18120/target_genomes_gtdb.txt
[2023-03-19 01:12:42,256] [INFO] Task started: fastANI
[2023-03-19 01:12:42,257] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcaa3824-d1f2-45f1-8e2d-b502123fd56c/OceanDNA-b18120.fa --refList OceanDNA-b18120/target_genomes_gtdb.txt --output OceanDNA-b18120/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:12:44,338] [INFO] Task succeeded: fastANI
[2023-03-19 01:12:44,345] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:12:44,346] [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_902578385.1	s__Marinisoma sp002710515	79.8278	142	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
GCA_902576865.1	s__Marinisoma sp902576865	79.6739	116	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.64	96.64	0.80	0.80	2	-
GCA_902525615.1	s__Marinisoma sp902525615	79.6033	137	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902538565.1	s__Marinisoma sp902538565	79.4281	159	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.07	99.04	0.96	0.96	3	-
GCA_016777965.1	s__Marinisoma sp016777965	79.3658	75	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599655.1	s__Marinisoma sp902599655	79.3334	109	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.53	97.28	0.66	0.66	3	-
GCA_000402655.1	s__Marinisoma sp000402655	79.2588	159	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
GCA_902624575.1	s__Marinisoma sp902624575	79.0001	79	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624275.1	s__Marinisoma sp902624275	78.9533	138	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902629855.1	s__Marinisoma sp902629855	78.7367	113	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	98.59	98.03	0.85	0.83	5	-
GCA_000402815.1	s__Marinisoma atlanticum	78.6453	74	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_905182795.1	s__Marinisoma sp905182795	77.4145	81	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902575395.1	s__Marinisoma sp902575395	76.99	53	231	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:12:44,346] [INFO] GTDB search result was written to OceanDNA-b18120/result_gtdb.tsv
[2023-03-19 01:12:44,346] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:12:44,347] [INFO] DFAST_QC result json was written to OceanDNA-b18120/dqc_result.json
[2023-03-19 01:12:44,347] [INFO] DFAST_QC completed!
[2023-03-19 01:12:44,347] [INFO] Total running time: 0h0m29s