[2023-03-16 16:43:21,347] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:43:21,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:43:21,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg598d5b27-d0a2-488c-89b0-329343a45655/dqc_reference
[2023-03-16 16:43:22,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:43:22,503] [INFO] Task started: Prodigal
[2023-03-16 16:43:22,503] [INFO] Running command: cat /var/lib/cwl/stg63a64622-5959-4b41-bb2c-3363ac90d89e/OceanDNA-b30011.fa | prodigal -d OceanDNA-b30011/cds.fna -a OceanDNA-b30011/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:43:37,011] [INFO] Task succeeded: Prodigal
[2023-03-16 16:43:37,012] [INFO] Task started: HMMsearch
[2023-03-16 16:43:37,012] [INFO] Running command: hmmsearch --tblout OceanDNA-b30011/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg598d5b27-d0a2-488c-89b0-329343a45655/dqc_reference/reference_markers.hmm OceanDNA-b30011/protein.faa > /dev/null
[2023-03-16 16:43:37,173] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:43:37,174] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg63a64622-5959-4b41-bb2c-3363ac90d89e/OceanDNA-b30011.fa]
[2023-03-16 16:43:37,190] [INFO] Query marker FASTA was written to OceanDNA-b30011/markers.fasta
[2023-03-16 16:43:37,192] [INFO] Task started: Blastn
[2023-03-16 16:43:37,192] [INFO] Running command: blastn -query OceanDNA-b30011/markers.fasta -db /var/lib/cwl/stg598d5b27-d0a2-488c-89b0-329343a45655/dqc_reference/reference_markers.fasta -out OceanDNA-b30011/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:43:37,746] [INFO] Task succeeded: Blastn
[2023-03-16 16:43:37,746] [INFO] Selected 12 target genomes.
[2023-03-16 16:43:37,747] [INFO] Target genome list was writen to OceanDNA-b30011/target_genomes.txt
[2023-03-16 16:43:37,777] [INFO] Task started: fastANI
[2023-03-16 16:43:37,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg63a64622-5959-4b41-bb2c-3363ac90d89e/OceanDNA-b30011.fa --refList OceanDNA-b30011/target_genomes.txt --output OceanDNA-b30011/fastani_result.tsv --threads 1
[2023-03-16 16:43:51,968] [INFO] Task succeeded: fastANI
[2023-03-16 16:43:51,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg598d5b27-d0a2-488c-89b0-329343a45655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:43:51,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg598d5b27-d0a2-488c-89b0-329343a45655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:43:51,977] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 16:43:51,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 16:43:51,977] [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
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	97.4497	611	625	95	conclusive
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	97.4215	615	625	95	conclusive
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	82.7092	457	625	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.4383	339	625	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	79.4205	311	625	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.4143	341	625	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.4237	234	625	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.534	210	625	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.4408	223	625	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.2269	151	625	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.0217	177	625	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.9943	153	625	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:43:51,977] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30011/tc_result.tsv
[2023-03-16 16:43:51,977] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:43:51,977] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:43:51,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg598d5b27-d0a2-488c-89b0-329343a45655/dqc_reference/checkm_data
[2023-03-16 16:43:51,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:43:51,992] [INFO] Task started: CheckM
[2023-03-16 16:43:51,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30011/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30011/checkm_input OceanDNA-b30011/checkm_result
[2023-03-16 16:44:26,021] [INFO] Task succeeded: CheckM
[2023-03-16 16:44:26,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:44:26,023] [INFO] ===== Completeness check finished =====
[2023-03-16 16:44:26,024] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:44:26,024] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30011/markers.fasta)
[2023-03-16 16:44:26,025] [INFO] Task started: Blastn
[2023-03-16 16:44:26,025] [INFO] Running command: blastn -query OceanDNA-b30011/markers.fasta -db /var/lib/cwl/stg598d5b27-d0a2-488c-89b0-329343a45655/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30011/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:44:26,695] [INFO] Task succeeded: Blastn
[2023-03-16 16:44:26,696] [INFO] Selected 7 target genomes.
[2023-03-16 16:44:26,696] [INFO] Target genome list was writen to OceanDNA-b30011/target_genomes_gtdb.txt
[2023-03-16 16:44:26,814] [INFO] Task started: fastANI
[2023-03-16 16:44:26,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg63a64622-5959-4b41-bb2c-3363ac90d89e/OceanDNA-b30011.fa --refList OceanDNA-b30011/target_genomes_gtdb.txt --output OceanDNA-b30011/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:44:31,910] [INFO] Task succeeded: fastANI
[2023-03-16 16:44:31,916] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:44:31,916] [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_900109195.1	s__Pseudooceanicola nitratireducens	97.4497	611	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	conclusive
GCF_004959925.1	s__Pseudooceanicola onchidii	82.6911	458	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	81.2924	435	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_000152725.1	s__Pseudooceanicola batsensis	81.1367	418	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	80.6175	416	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	79.3333	346	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCA_002709085.1	s__Pseudooceanicola sp002709085	79.1657	241	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:44:31,916] [INFO] GTDB search result was written to OceanDNA-b30011/result_gtdb.tsv
[2023-03-16 16:44:31,916] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:44:31,918] [INFO] DFAST_QC result json was written to OceanDNA-b30011/dqc_result.json
[2023-03-16 16:44:31,918] [INFO] DFAST_QC completed!
[2023-03-16 16:44:31,918] [INFO] Total running time: 0h1m11s