[2023-03-18 08:55:50,694] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,694] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc8a5235-c037-4d05-8272-a3eedd072ac8/dqc_reference
[2023-03-18 08:55:51,904] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,904] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,904] [INFO] Running command: cat /var/lib/cwl/stg517d004f-eeb9-4620-b214-3444e0257d04/OceanDNA-b9486.fa | prodigal -d OceanDNA-b9486/cds.fna -a OceanDNA-b9486/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:04,425] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:04,425] [INFO] Task started: HMMsearch
[2023-03-18 08:56:04,425] [INFO] Running command: hmmsearch --tblout OceanDNA-b9486/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc8a5235-c037-4d05-8272-a3eedd072ac8/dqc_reference/reference_markers.hmm OceanDNA-b9486/protein.faa > /dev/null
[2023-03-18 08:56:04,628] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:04,629] [INFO] Found 6/6 markers.
[2023-03-18 08:56:04,641] [INFO] Query marker FASTA was written to OceanDNA-b9486/markers.fasta
[2023-03-18 08:56:04,641] [INFO] Task started: Blastn
[2023-03-18 08:56:04,642] [INFO] Running command: blastn -query OceanDNA-b9486/markers.fasta -db /var/lib/cwl/stgcc8a5235-c037-4d05-8272-a3eedd072ac8/dqc_reference/reference_markers.fasta -out OceanDNA-b9486/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:05,238] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:05,239] [INFO] Selected 33 target genomes.
[2023-03-18 08:56:05,240] [INFO] Target genome list was writen to OceanDNA-b9486/target_genomes.txt
[2023-03-18 08:56:05,262] [INFO] Task started: fastANI
[2023-03-18 08:56:05,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg517d004f-eeb9-4620-b214-3444e0257d04/OceanDNA-b9486.fa --refList OceanDNA-b9486/target_genomes.txt --output OceanDNA-b9486/fastani_result.tsv --threads 1
[2023-03-18 08:56:24,949] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:24,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc8a5235-c037-4d05-8272-a3eedd072ac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:24,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc8a5235-c037-4d05-8272-a3eedd072ac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:24,953] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:24,953] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:56:24,953] [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
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	75.9692	52	603	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:56:24,954] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9486/tc_result.tsv
[2023-03-18 08:56:24,954] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:24,954] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:24,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc8a5235-c037-4d05-8272-a3eedd072ac8/dqc_reference/checkm_data
[2023-03-18 08:56:24,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:24,996] [INFO] Task started: CheckM
[2023-03-18 08:56:24,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9486/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9486/checkm_input OceanDNA-b9486/checkm_result
[2023-03-18 08:56:59,074] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:59,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:59,077] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:59,078] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:59,078] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9486/markers.fasta)
[2023-03-18 08:56:59,079] [INFO] Task started: Blastn
[2023-03-18 08:56:59,079] [INFO] Running command: blastn -query OceanDNA-b9486/markers.fasta -db /var/lib/cwl/stgcc8a5235-c037-4d05-8272-a3eedd072ac8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9486/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:59,866] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:59,868] [INFO] Selected 21 target genomes.
[2023-03-18 08:56:59,868] [INFO] Target genome list was writen to OceanDNA-b9486/target_genomes_gtdb.txt
[2023-03-18 08:56:59,907] [INFO] Task started: fastANI
[2023-03-18 08:56:59,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg517d004f-eeb9-4620-b214-3444e0257d04/OceanDNA-b9486.fa --refList OceanDNA-b9486/target_genomes_gtdb.txt --output OceanDNA-b9486/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:57:07,209] [INFO] Task succeeded: fastANI
[2023-03-18 08:57:07,219] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:57:07,220] [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_000173095.1	s__MS024-2A sp000173095	99.6079	536	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	conclusive
GCA_905181895.1	s__MS024-2A sp905181895	80.5134	230	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	79.7929	369	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292265.1	s__MS024-2A sp002292265	79.0994	129	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
GCA_905182305.1	s__MS024-2A sp905182305	78.1827	224	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480425.1	s__MS024-2A sp905480425	77.9641	221	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_017851655.1	s__MS024-2A sp017851655	77.1895	149	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_011525195.1	s__MS024-2A sp011525195	77.1565	101	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699935.1	s__MS024-2A sp018699935	77.0965	84	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.36	99.36	0.92	0.92	2	-
GCA_017858055.1	s__MS024-2A sp002384715	77.0587	119	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
GCA_902546725.1	s__MS024-2A sp902546725	77.0111	103	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167945.1	s__MS024-2A sp002167945	76.8175	112	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181615.1	s__UBA7428 sp905181615	76.7267	70	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_902517245.1	s__MS024-2A sp902517245	76.4297	80	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857815.1	s__UBA8316 sp017857815	76.415	61	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616905.1	s__MS024-2A sp902616905	76.2805	77	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512755.1	s__MS024-2A sp902512755	76.176	78	603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:57:07,221] [INFO] GTDB search result was written to OceanDNA-b9486/result_gtdb.tsv
[2023-03-18 08:57:07,221] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:57:07,222] [INFO] DFAST_QC result json was written to OceanDNA-b9486/dqc_result.json
[2023-03-18 08:57:07,222] [INFO] DFAST_QC completed!
[2023-03-18 08:57:07,222] [INFO] Total running time: 0h1m17s