[2023-03-16 07:55:45,164] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:55:45,164] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:55:45,165] [INFO] DQC Reference Directory: /var/lib/cwl/stgc735bcc4-f3c0-4bf5-975c-f6c792fcad2f/dqc_reference
[2023-03-16 07:55:46,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:55:46,308] [INFO] Task started: Prodigal
[2023-03-16 07:55:46,309] [INFO] Running command: cat /var/lib/cwl/stg16c5b989-7d51-418e-82a4-71e0b6958ad2/OceanDNA-b7538.fa | prodigal -d OceanDNA-b7538/cds.fna -a OceanDNA-b7538/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:56:14,882] [INFO] Task succeeded: Prodigal
[2023-03-16 07:56:14,882] [INFO] Task started: HMMsearch
[2023-03-16 07:56:14,882] [INFO] Running command: hmmsearch --tblout OceanDNA-b7538/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc735bcc4-f3c0-4bf5-975c-f6c792fcad2f/dqc_reference/reference_markers.hmm OceanDNA-b7538/protein.faa > /dev/null
[2023-03-16 07:56:15,107] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:56:15,108] [INFO] Found 6/6 markers.
[2023-03-16 07:56:15,133] [INFO] Query marker FASTA was written to OceanDNA-b7538/markers.fasta
[2023-03-16 07:56:15,134] [INFO] Task started: Blastn
[2023-03-16 07:56:15,134] [INFO] Running command: blastn -query OceanDNA-b7538/markers.fasta -db /var/lib/cwl/stgc735bcc4-f3c0-4bf5-975c-f6c792fcad2f/dqc_reference/reference_markers.fasta -out OceanDNA-b7538/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:56:15,737] [INFO] Task succeeded: Blastn
[2023-03-16 07:56:15,738] [INFO] Selected 18 target genomes.
[2023-03-16 07:56:15,738] [INFO] Target genome list was writen to OceanDNA-b7538/target_genomes.txt
[2023-03-16 07:56:15,777] [INFO] Task started: fastANI
[2023-03-16 07:56:15,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c5b989-7d51-418e-82a4-71e0b6958ad2/OceanDNA-b7538.fa --refList OceanDNA-b7538/target_genomes.txt --output OceanDNA-b7538/fastani_result.tsv --threads 1
[2023-03-16 07:56:28,092] [INFO] Task succeeded: fastANI
[2023-03-16 07:56:28,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc735bcc4-f3c0-4bf5-975c-f6c792fcad2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:56:28,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc735bcc4-f3c0-4bf5-975c-f6c792fcad2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:56:28,102] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:56:28,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:56:28,102] [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
Leeuwenhoekiella nanhaiensis	strain=G18	GCA_002744755.1	1655491	1655491	type	True	84.0897	1053	1390	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	81.7139	623	1390	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	78.9606	483	1390	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	78.6132	547	1390	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	78.6003	537	1390	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	78.3524	466	1390	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	78.3448	478	1390	95	below_threshold
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	77.7515	295	1390	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_000769435.1	326320	326320	type	True	76.3268	55	1390	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_001653755.1	326320	326320	type	True	76.2959	56	1390	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.268	70	1390	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	75.9271	78	1390	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.7265	59	1390	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	75.6418	53	1390	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:56:28,131] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7538/tc_result.tsv
[2023-03-16 07:56:28,131] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:56:28,131] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:56:28,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc735bcc4-f3c0-4bf5-975c-f6c792fcad2f/dqc_reference/checkm_data
[2023-03-16 07:56:28,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:56:28,140] [INFO] Task started: CheckM
[2023-03-16 07:56:28,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7538/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7538/checkm_input OceanDNA-b7538/checkm_result
[2023-03-16 07:57:38,335] [INFO] Task succeeded: CheckM
[2023-03-16 07:57:38,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:57:38,408] [INFO] ===== Completeness check finished =====
[2023-03-16 07:57:38,408] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:57:38,408] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7538/markers.fasta)
[2023-03-16 07:57:38,410] [INFO] Task started: Blastn
[2023-03-16 07:57:38,410] [INFO] Running command: blastn -query OceanDNA-b7538/markers.fasta -db /var/lib/cwl/stgc735bcc4-f3c0-4bf5-975c-f6c792fcad2f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7538/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:57:39,265] [INFO] Task succeeded: Blastn
[2023-03-16 07:57:39,266] [INFO] Selected 11 target genomes.
[2023-03-16 07:57:39,266] [INFO] Target genome list was writen to OceanDNA-b7538/target_genomes_gtdb.txt
[2023-03-16 07:57:39,332] [INFO] Task started: fastANI
[2023-03-16 07:57:39,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c5b989-7d51-418e-82a4-71e0b6958ad2/OceanDNA-b7538.fa --refList OceanDNA-b7538/target_genomes_gtdb.txt --output OceanDNA-b7538/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:57:48,652] [INFO] Task succeeded: fastANI
[2023-03-16 07:57:48,659] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:57:48,659] [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_002708845.1	s__Leeuwenhoekiella sp002708845	99.8996	1346	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	conclusive
GCF_002744755.1	s__Leeuwenhoekiella nanhaiensis	84.0811	1054	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	81.7104	624	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	81.4544	647	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	78.9563	484	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	78.5952	539	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	78.3614	464	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	77.8029	432	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104375.1	s__Leeuwenhoekiella aequorea	77.7489	296	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349235.1	s__Euzebyella sp014349235	76.3404	51	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653755.1	s__Dokdonia donghaensis	76.2959	56	1390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	97.85	95.71	0.96	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 07:57:48,663] [INFO] GTDB search result was written to OceanDNA-b7538/result_gtdb.tsv
[2023-03-16 07:57:48,664] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:57:48,665] [INFO] DFAST_QC result json was written to OceanDNA-b7538/dqc_result.json
[2023-03-16 07:57:48,665] [INFO] DFAST_QC completed!
[2023-03-16 07:57:48,665] [INFO] Total running time: 0h2m4s