[2023-03-17 00:45:47,173] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,173] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ee62fab-78ef-4159-b119-380e7b87e8bf/dqc_reference
[2023-03-17 00:45:48,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stg8c292974-583c-47bf-b77a-f313838a3d95/OceanDNA-b41510.fa | prodigal -d OceanDNA-b41510/cds.fna -a OceanDNA-b41510/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:03,176] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:03,177] [INFO] Task started: HMMsearch
[2023-03-17 00:46:03,177] [INFO] Running command: hmmsearch --tblout OceanDNA-b41510/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ee62fab-78ef-4159-b119-380e7b87e8bf/dqc_reference/reference_markers.hmm OceanDNA-b41510/protein.faa > /dev/null
[2023-03-17 00:46:03,380] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:03,381] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8c292974-583c-47bf-b77a-f313838a3d95/OceanDNA-b41510.fa]
[2023-03-17 00:46:03,405] [INFO] Query marker FASTA was written to OceanDNA-b41510/markers.fasta
[2023-03-17 00:46:03,406] [INFO] Task started: Blastn
[2023-03-17 00:46:03,406] [INFO] Running command: blastn -query OceanDNA-b41510/markers.fasta -db /var/lib/cwl/stg3ee62fab-78ef-4159-b119-380e7b87e8bf/dqc_reference/reference_markers.fasta -out OceanDNA-b41510/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:04,012] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:04,013] [INFO] Selected 21 target genomes.
[2023-03-17 00:46:04,013] [INFO] Target genome list was writen to OceanDNA-b41510/target_genomes.txt
[2023-03-17 00:46:04,059] [INFO] Task started: fastANI
[2023-03-17 00:46:04,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c292974-583c-47bf-b77a-f313838a3d95/OceanDNA-b41510.fa --refList OceanDNA-b41510/target_genomes.txt --output OceanDNA-b41510/fastani_result.tsv --threads 1
[2023-03-17 00:46:17,583] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:17,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ee62fab-78ef-4159-b119-380e7b87e8bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:17,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ee62fab-78ef-4159-b119-380e7b87e8bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:17,591] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:17,591] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:46:17,591] [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
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	82.3031	337	771	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	82.0924	82	771	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.8527	85	771	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	77.806	105	771	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.2152	65	771	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.1265	51	771	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	77.0484	50	771	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	77.0303	85	771	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.0091	50	771	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	76.1764	50	771	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:17,591] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41510/tc_result.tsv
[2023-03-17 00:46:17,591] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:17,591] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:17,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ee62fab-78ef-4159-b119-380e7b87e8bf/dqc_reference/checkm_data
[2023-03-17 00:46:17,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:17,597] [INFO] Task started: CheckM
[2023-03-17 00:46:17,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41510/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41510/checkm_input OceanDNA-b41510/checkm_result
[2023-03-17 00:46:57,890] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:57,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:57,893] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:57,893] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:57,893] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41510/markers.fasta)
[2023-03-17 00:46:57,894] [INFO] Task started: Blastn
[2023-03-17 00:46:57,894] [INFO] Running command: blastn -query OceanDNA-b41510/markers.fasta -db /var/lib/cwl/stg3ee62fab-78ef-4159-b119-380e7b87e8bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41510/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:58,767] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:58,767] [INFO] Selected 14 target genomes.
[2023-03-17 00:46:58,767] [INFO] Target genome list was writen to OceanDNA-b41510/target_genomes_gtdb.txt
[2023-03-17 00:46:58,976] [INFO] Task started: fastANI
[2023-03-17 00:46:58,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c292974-583c-47bf-b77a-f313838a3d95/OceanDNA-b41510.fa --refList OceanDNA-b41510/target_genomes_gtdb.txt --output OceanDNA-b41510/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:07,337] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:07,342] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:47:07,342] [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_014191715.1	s__Litorivivens lipolytica	82.3267	336	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710725.1	s__Litorivivens sp002710725	80.1408	242	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415025.1	s__Litorivivens sp002415025	78.1214	205	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	99.88	99.82	0.96	0.94	3	-
GCF_012272835.1	s__Spongiibacter sp012272835	77.806	105	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016906995.1	s__Spongiibacter marinus	77.2903	77	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	97.69	97.65	0.87	0.86	3	-
GCF_008064665.1	s__Parahaliea maris	77.1723	66	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016132545.1	s__CSC3-9 sp016132545	77.0303	85	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	76.473	64	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:07,342] [INFO] GTDB search result was written to OceanDNA-b41510/result_gtdb.tsv
[2023-03-17 00:47:07,343] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:07,344] [INFO] DFAST_QC result json was written to OceanDNA-b41510/dqc_result.json
[2023-03-17 00:47:07,344] [INFO] DFAST_QC completed!
[2023-03-17 00:47:07,344] [INFO] Total running time: 0h1m20s