[2023-03-15 19:39:18,204] [INFO] DFAST_QC pipeline started.
[2023-03-15 19:39:18,204] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 19:39:18,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg662b4d98-4415-447c-a569-269b2ae29d3c/dqc_reference
[2023-03-15 19:39:19,430] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 19:39:19,431] [INFO] Task started: Prodigal
[2023-03-15 19:39:19,431] [INFO] Running command: cat /var/lib/cwl/stg2ae2bfd8-7772-46d4-a503-27572cd8dbb5/OceanDNA-b7494.fa | prodigal -d OceanDNA-b7494/cds.fna -a OceanDNA-b7494/protein.faa -g 11 -q > /dev/null
[2023-03-15 19:39:46,080] [INFO] Task succeeded: Prodigal
[2023-03-15 19:39:46,080] [INFO] Task started: HMMsearch
[2023-03-15 19:39:46,081] [INFO] Running command: hmmsearch --tblout OceanDNA-b7494/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg662b4d98-4415-447c-a569-269b2ae29d3c/dqc_reference/reference_markers.hmm OceanDNA-b7494/protein.faa > /dev/null
[2023-03-15 19:39:46,299] [INFO] Task succeeded: HMMsearch
[2023-03-15 19:39:46,300] [INFO] Found 6/6 markers.
[2023-03-15 19:39:46,323] [INFO] Query marker FASTA was written to OceanDNA-b7494/markers.fasta
[2023-03-15 19:39:46,324] [INFO] Task started: Blastn
[2023-03-15 19:39:46,325] [INFO] Running command: blastn -query OceanDNA-b7494/markers.fasta -db /var/lib/cwl/stg662b4d98-4415-447c-a569-269b2ae29d3c/dqc_reference/reference_markers.fasta -out OceanDNA-b7494/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:39:47,093] [INFO] Task succeeded: Blastn
[2023-03-15 19:39:47,094] [INFO] Selected 23 target genomes.
[2023-03-15 19:39:47,094] [INFO] Target genome list was writen to OceanDNA-b7494/target_genomes.txt
[2023-03-15 19:39:47,106] [INFO] Task started: fastANI
[2023-03-15 19:39:47,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae2bfd8-7772-46d4-a503-27572cd8dbb5/OceanDNA-b7494.fa --refList OceanDNA-b7494/target_genomes.txt --output OceanDNA-b7494/fastani_result.tsv --threads 1
[2023-03-15 19:40:00,623] [INFO] Task succeeded: fastANI
[2023-03-15 19:40:00,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg662b4d98-4415-447c-a569-269b2ae29d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 19:40:00,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg662b4d98-4415-447c-a569-269b2ae29d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 19:40:00,629] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 19:40:00,629] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 19:40:00,629] [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 marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	76.9305	88	1153	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	76.6622	71	1153	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	76.3476	74	1153	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	76.3374	77	1153	95	below_threshold
Leeuwenhoekiella nanhaiensis	strain=G18	GCA_002744755.1	1655491	1655491	type	True	76.1791	80	1153	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	76.1153	69	1153	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 19:40:00,630] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7494/tc_result.tsv
[2023-03-15 19:40:00,630] [INFO] ===== Taxonomy check completed =====
[2023-03-15 19:40:00,630] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 19:40:00,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg662b4d98-4415-447c-a569-269b2ae29d3c/dqc_reference/checkm_data
[2023-03-15 19:40:00,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 19:40:00,636] [INFO] Task started: CheckM
[2023-03-15 19:40:00,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7494/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7494/checkm_input OceanDNA-b7494/checkm_result
[2023-03-15 19:41:07,208] [INFO] Task succeeded: CheckM
[2023-03-15 19:41:07,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.03%
Contamintation: 1.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 19:41:07,211] [INFO] ===== Completeness check finished =====
[2023-03-15 19:41:07,211] [INFO] ===== Start GTDB Search =====
[2023-03-15 19:41:07,211] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7494/markers.fasta)
[2023-03-15 19:41:07,213] [INFO] Task started: Blastn
[2023-03-15 19:41:07,213] [INFO] Running command: blastn -query OceanDNA-b7494/markers.fasta -db /var/lib/cwl/stg662b4d98-4415-447c-a569-269b2ae29d3c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7494/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:41:08,266] [INFO] Task succeeded: Blastn
[2023-03-15 19:41:08,267] [INFO] Selected 24 target genomes.
[2023-03-15 19:41:08,267] [INFO] Target genome list was writen to OceanDNA-b7494/target_genomes_gtdb.txt
[2023-03-15 19:41:08,840] [INFO] Task started: fastANI
[2023-03-15 19:41:08,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae2bfd8-7772-46d4-a503-27572cd8dbb5/OceanDNA-b7494.fa --refList OceanDNA-b7494/target_genomes_gtdb.txt --output OceanDNA-b7494/fastani_result_gtdb.tsv --threads 1
[2023-03-15 19:41:23,231] [INFO] Task succeeded: fastANI
[2023-03-15 19:41:23,236] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 19:41:23,236] [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_000733945.1	s__Leeuwenhoekiella sp000733945	77.8344	157	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710685.1	s__Leeuwenhoekiella sp002710685	77.5484	93	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	77.1479	85	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	76.6622	71	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	76.3476	74	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	76.3311	76	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_002744755.1	s__Leeuwenhoekiella nanhaiensis	76.2245	81	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-03-15 19:41:23,236] [INFO] GTDB search result was written to OceanDNA-b7494/result_gtdb.tsv
[2023-03-15 19:41:23,236] [INFO] ===== GTDB Search completed =====
[2023-03-15 19:41:23,238] [INFO] DFAST_QC result json was written to OceanDNA-b7494/dqc_result.json
[2023-03-15 19:41:23,238] [INFO] DFAST_QC completed!
[2023-03-15 19:41:23,238] [INFO] Total running time: 0h2m5s