[2023-03-16 17:56:33,743] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:56:33,743] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:56:33,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdc13fa2-5892-40d1-a260-0e5309adc65a/dqc_reference
[2023-03-16 17:56:35,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:56:35,080] [INFO] Task started: Prodigal
[2023-03-16 17:56:35,080] [INFO] Running command: cat /var/lib/cwl/stg05d6686c-16d8-4de9-8e93-3c5dea7aa1cb/OceanDNA-b41476.fa | prodigal -d OceanDNA-b41476/cds.fna -a OceanDNA-b41476/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:57:06,776] [INFO] Task succeeded: Prodigal
[2023-03-16 17:57:06,776] [INFO] Task started: HMMsearch
[2023-03-16 17:57:06,776] [INFO] Running command: hmmsearch --tblout OceanDNA-b41476/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdc13fa2-5892-40d1-a260-0e5309adc65a/dqc_reference/reference_markers.hmm OceanDNA-b41476/protein.faa > /dev/null
[2023-03-16 17:57:06,985] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:57:06,986] [INFO] Found 6/6 markers.
[2023-03-16 17:57:07,010] [INFO] Query marker FASTA was written to OceanDNA-b41476/markers.fasta
[2023-03-16 17:57:07,011] [INFO] Task started: Blastn
[2023-03-16 17:57:07,011] [INFO] Running command: blastn -query OceanDNA-b41476/markers.fasta -db /var/lib/cwl/stgcdc13fa2-5892-40d1-a260-0e5309adc65a/dqc_reference/reference_markers.fasta -out OceanDNA-b41476/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:57:07,710] [INFO] Task succeeded: Blastn
[2023-03-16 17:57:07,711] [INFO] Selected 27 target genomes.
[2023-03-16 17:57:07,712] [INFO] Target genome list was writen to OceanDNA-b41476/target_genomes.txt
[2023-03-16 17:57:07,727] [INFO] Task started: fastANI
[2023-03-16 17:57:07,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d6686c-16d8-4de9-8e93-3c5dea7aa1cb/OceanDNA-b41476.fa --refList OceanDNA-b41476/target_genomes.txt --output OceanDNA-b41476/fastani_result.tsv --threads 1
[2023-03-16 17:57:25,084] [INFO] Task succeeded: fastANI
[2023-03-16 17:57:25,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdc13fa2-5892-40d1-a260-0e5309adc65a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:57:25,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdc13fa2-5892-40d1-a260-0e5309adc65a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:57:25,091] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:57:25,091] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:57:25,091] [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
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	79.1195	405	1191	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	78.0378	266	1191	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.7006	176	1191	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.1654	199	1191	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	77.1568	216	1191	95	below_threshold
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	76.8503	116	1191	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	75.9576	50	1191	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:57:25,091] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41476/tc_result.tsv
[2023-03-16 17:57:25,091] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:57:25,092] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:57:25,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdc13fa2-5892-40d1-a260-0e5309adc65a/dqc_reference/checkm_data
[2023-03-16 17:57:25,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:57:25,144] [INFO] Task started: CheckM
[2023-03-16 17:57:25,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41476/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41476/checkm_input OceanDNA-b41476/checkm_result
[2023-03-16 17:58:20,476] [INFO] Task succeeded: CheckM
[2023-03-16 17:58:20,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:58:20,478] [INFO] ===== Completeness check finished =====
[2023-03-16 17:58:20,478] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:58:20,479] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41476/markers.fasta)
[2023-03-16 17:58:20,480] [INFO] Task started: Blastn
[2023-03-16 17:58:20,480] [INFO] Running command: blastn -query OceanDNA-b41476/markers.fasta -db /var/lib/cwl/stgcdc13fa2-5892-40d1-a260-0e5309adc65a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41476/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:58:21,771] [INFO] Task succeeded: Blastn
[2023-03-16 17:58:21,771] [INFO] Selected 16 target genomes.
[2023-03-16 17:58:21,772] [INFO] Target genome list was writen to OceanDNA-b41476/target_genomes_gtdb.txt
[2023-03-16 17:58:21,788] [INFO] Task started: fastANI
[2023-03-16 17:58:21,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d6686c-16d8-4de9-8e93-3c5dea7aa1cb/OceanDNA-b41476.fa --refList OceanDNA-b41476/target_genomes_gtdb.txt --output OceanDNA-b41476/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:58:32,788] [INFO] Task succeeded: fastANI
[2023-03-16 17:58:32,794] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:58:32,794] [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_016906995.1	s__Spongiibacter marinus	97.7846	1008	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	97.69	97.65	0.87	0.86	3	conclusive
GCF_000422345.1	s__Spongiibacter marinus_A	94.6083	993	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420325.1	s__Spongiibacter tropicus	79.1318	403	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCF_012272835.1	s__Spongiibacter sp012272835	78.0378	266	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705705.1	s__KMU-158 sp014705705	77.7006	176	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016132545.1	s__CSC3-9 sp016132545	77.1568	216	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705875.1	s__Marortus aliphaticivorans_A	76.8667	111	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-16 17:58:32,794] [INFO] GTDB search result was written to OceanDNA-b41476/result_gtdb.tsv
[2023-03-16 17:58:32,794] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:58:32,795] [INFO] DFAST_QC result json was written to OceanDNA-b41476/dqc_result.json
[2023-03-16 17:58:32,795] [INFO] DFAST_QC completed!
[2023-03-16 17:58:32,795] [INFO] Total running time: 0h1m59s